Datasets:

lanesket

/

r-asts

like 0

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){utils.hwe}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){prob}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Detected Presence/Absence (S...}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){ applies only to SNP data!\n}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Dataset contains mo...}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){ calculations\n}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){hom.ref}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){m}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){hom.snp}<LSEP>[](symbol){hom.ref}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){het}<LSEP>[](symbol){hom.ref}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){total}<LSEP>[](symbol){hom.ref}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){p.values}<LSEP>[](symbol){hom.ref}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){boncrit}<LSEP>[](symbol){hom.ref}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){sig}<LSEP>[](symbol){hom.ref}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){sig2}<LSEP>[](symbol){hom.ref}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){bonsig}<LSEP>[](symbol){hom.ref}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){bonsig2}<LSEP>[](symbol){hom.ref}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){columns}<LEND>[call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){m}<LEND>[statement 20; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.ref}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.snp}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){het}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){utils.prob.hwe}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){het}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.ref}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.snp}<LSEP>[](symbol){i}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sig2}<LSEP>[](symbol){i}<LEND>[litteral](logical){NA}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.050000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sig2}<LSEP>[](symbol){i}<LEND>[litteral](str){ns}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.050000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.010000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sig2}<LSEP>[](symbol){i}<LEND>[litteral](str){*}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.010000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.001000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sig2}<LSEP>[](symbol){i}<LEND>[litteral](str){**}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.001000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sig2}<LSEP>[](symbol){i}<LEND>[litteral](str){***}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){total}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.ref}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){het}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.snp}<LSEP>[](symbol){i}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){boncrit}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){prob}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){total}<LSEP>[](symbol){i}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){boncrit}<LSEP>[](symbol){i}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig2}<LSEP>[](symbol){i}<LEND>[litteral](str){ns}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig2}<LSEP>[](symbol){i}<LEND>[litteral](str){*}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){hom.ref}<LSEP>[](symbol){het}<LSEP>[](symbol){hom.snp}<LSEP>[](symbol){total}<LSEP>[](symbol){p.values}<LSEP>[](symbol){sig2}<LSEP>[](symbol){bonsig2}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){columns}<LSEP>[](symbol){result}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Locus}<LSEP>[argument 1; litteral](str){Hom_1}<LSEP>[argument 2; litteral](str){Het}<LSEP>[argument 3; litteral](str){Hom_2}<LSEP>[argument 4; litteral](str){N}<LSEP>[argument 5; litteral](str){Prob}<LSEP>[argument 6; litteral](str){Sig}<LSEP>[argument 7; litteral](str){BonSig}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){pc}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){sig}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){sig}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){pc}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){pc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){pc2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){bonsig}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){bonsig}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){pc2}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){pc2}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 29; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){result}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){cramer.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){check}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ is not a data.frame}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){check}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){x[, }<LSEP>[](symbol){k1}<LSEP>[argument 2; litteral](str){] is converted to a factor}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){assoc}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){CramerV}<LSEP>[](symbol){x1}<LSEP>[](symbol){x1}<LSEP>[argument 2; litteral](logical){NA}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k2}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){k1}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k2}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k2}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){CramerV}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LSEP>[argument 2; litteral](logical){NA}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}<LEND>[assign](){<-}<LSEP>[](symbol){tschuprow.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){check}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ is not a data.frame}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){check}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){x[, }<LSEP>[](symbol){k1}<LSEP>[argument 2; litteral](str){] is converted to a factor}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){assoc}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){TschuprowT}<LSEP>[](symbol){x1}<LSEP>[](symbol){x1}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k2}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){k1}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k2}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k2}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){TschuprowT}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}<LEND>[assign](){<-}<LSEP>[](symbol){pearson.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){check}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ is not a data.frame}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){check}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){x[, }<LSEP>[](symbol){k1}<LSEP>[argument 2; litteral](str){] is converted to a factor}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){assoc}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){ContCoef}<LSEP>[](symbol){x1}<LSEP>[](symbol){x1}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k2}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){k1}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k2}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k2}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){ContCoef}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}<LEND>[assign](){<-}<LSEP>[](symbol){phi.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){check}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ is not a data.frame}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){check}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){x[, }<LSEP>[](symbol){k1}<LSEP>[argument 2; litteral](str){] is converted to a factor}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){assoc}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){Phi}<LSEP>[](symbol){x1}<LSEP>[](symbol){x1}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k2}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){k1}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k2}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k2}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){Phi}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){warpArea}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){d}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.dtw}<LSEP>[](symbol){d}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){dtw object required}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ii}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stats}<LSEP>[](symbol){approx}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index2}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){N}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dg}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){M}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){N}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){ad}<LEND>[call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ii}<LSEP>[](symbol){y}<LEND>[](symbol){dg}<LEND>[statement 4; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){ad}<LEND>[assign](){<-}<LSEP>[](symbol){.localWarpingStretch}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){d}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){id1}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index1}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){id2}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index2}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){id2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){id2}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){M}<LEND>[statement 3; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){id1}<LSEP>[](symbol){id2}<LEND>[assign](){<-}<LSEP>[](symbol){.localWarpingCost}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){d}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){localCostMatrix}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){A dtw object with keep.interna...}<LEND>[statement 1; call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){localCostMatrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index1}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index2}

[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){ada.formula}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){formula}<LSEP>[](symbol){data}<LSEP>[](symbol){...}<LSEP>[](symbol){subset}<LSEP>[](symbol){na.action}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){match.call}<LSEP>[argument 0; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){model}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){method}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){control}<LEND>[litteral](NULL){NULL}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){y}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){parms}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){...}<LEND>[litteral](NULL){NULL}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){cost}<LEND>[litteral](NULL){NULL}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){na.action}<LEND>[](symbol){na.action}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){model.frame}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){eval}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){parent.frame}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){Terms}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](str){terms}<LEND>[statement 8; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){model.extract}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](str){response}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){preds}<LEND>[call](){}<LSEP>[](symbol){attr}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){m}<LEND>[](symbol){terms}<LEND>[argument 1; litteral](str){term.labels}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){preds}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){vec}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){m}<LEND>[](symbol){preds}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){vec}<LEND>[statement 2; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[](symbol){preds}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){m}<LEND>[](symbol){preds}<LEND>[statement 11; assign](){=}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){ada.default}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){...}<LSEP>[](symbol){na.action}<LEND>[statement 12; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){res}<LSEP>[](symbol){terms}<LEND>[](symbol){Terms}<LEND>[statement 13; assign](){=}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 14; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cl}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){ada}<LEND>[statement 15; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){res}<LSEP>[](symbol){call}<LEND>[](symbol){cl}<LEND>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.refstocksurl}<LSEP>[litteral](str){https://api.twelvedata.com/stocks}<LEND>[assign](){<-}<LSEP>[](symbol){ref_stocks}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){sym}<LSEP>[](symbol){as}<LSEP>[](symbol){exchange}<LSEP>[](symbol){country}<LSEP>[](symbol){type}<LSEP>[](symbol){apikey}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){apikey}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){apikey}<LEND>[call](){}<LSEP>[](symbol){.get_apikey}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){as}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){as}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){type}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){.refstocksurl}<LSEP>[argument 1; litteral](str){?}<LSEP>[argument 2; litteral](str){&apikey=}<LSEP>[](symbol){apikey}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sym}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&symbol=}<LSEP>[](symbol){sym}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){exchange}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&exchange=}<LSEP>[](symbol){exchange}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){country}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&country=}<LSEP>[](symbol){country}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&type=}<LSEP>[](symbol){type}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){accessed}<LEND>[call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[argument 1; litteral](str){UTC}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RcppSimdJson}<LSEP>[](symbol){fload}<LEND>[](symbol){qry}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){as}<LSEP>[argument 1; litteral](str){raw}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){sym}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){res}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[](symbol){sym}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){res}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){status}<LEND>[argument 1; litteral](str){ok}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){message}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){data}<LEND>[](symbol){dat}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[argument 0; litteral](str){rbind}<LSEP>[](symbol){dat}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){dat}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The API returned NULL. Try to ...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dat}<LSEP>[argument 1; litteral](str){accessed}<LEND>[](symbol){accessed}<LEND>[](symbol){dat}

[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){dht}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){inverted}<LEND>[body; call](){}<LSEP>[](symbol){dtt}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){dht}<LSEP>[](symbol){inverted}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.read.dart}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){filename}<LSEP>[](symbol){ind.metafile}<LSEP>[](symbol){recalc}<LSEP>[](symbol){mono.rm}<LSEP>[](symbol){nas}<LSEP>[](symbol){topskip}<LSEP>[](symbol){lastmetric}<LSEP>[](symbol){covfilename}<LSEP>[](symbol){probar}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){probar}<LSEP>[litteral](logical){FALSE}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ind.metafile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ind.metafile}<LSEP>[](symbol){covfilename}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){dout}<LEND>[call](){}<LSEP>[](symbol){utils.read.dart}<LSEP>[](symbol){filename}<LSEP>[](symbol){nas}<LSEP>[](symbol){topskip}<LSEP>[](symbol){lastmetric}<LSEP>[](symbol){verbose}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){glout}<LEND>[call](){}<LSEP>[](symbol){utils.dart2genlight}<LSEP>[](symbol){dout}<LSEP>[](symbol){ind.metafile}<LSEP>[](symbol){probar}<LSEP>[](symbol){verbose}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Data read in. Please check ca...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){recalc.flags}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){AvgPIC}<LSEP>[argument 1; litteral](str){OneRatioRef}<LSEP>[argument 2; litteral](str){OneRatioSnp}<LSEP>[argument 3; litteral](str){PICRef}<LSEP>[argument 4; litteral](str){PICSnp}<LSEP>[argument 5; litteral](str){CallRate}<LSEP>[argument 6; litteral](str){maf}<LSEP>[argument 7; litteral](str){FreqHets}<LSEP>[argument 8; litteral](str){FreqHomRef}<LSEP>[argument 9; litteral](str){FreqHomSnp}<LSEP>[argument 10; litteral](str){monomorphs}<LSEP>[argument 11; litteral](str){OneRatio}<LSEP>[argument 12; litteral](str){PIC}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){TRUE}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){recalc.flags}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){recalc.flags}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[litteral](real){2.000000}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){rdepth}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Read depth calculated and ad...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){rdepth}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){glout}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){glout}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){called.ind}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){glout}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){CallRate}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ref.count}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){called.ind}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatioRef}<LEND>[](symbol){i}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){alt.count}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){called.ind}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatioSnp}<LEND>[](symbol){i}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){sum.count.ref}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){ref.count}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){AvgCountRef}<LEND>[](symbol){i}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){sum.count.alt}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){alt.count}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){AvgCountSnp}<LEND>[](symbol){i}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){rdepth}<LEND>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){sum.count.alt}<LSEP>[](symbol){sum.count.ref}<LEND>[](symbol){called.ind}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){maf}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){utils.recalc.maf}<LSEP>[](symbol){glout}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Minor Allele Frequency (maf)...}<LEND>[statement 16; control flow](){if}<LSEP>[](symbol){recalc}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Recalculating locus metrics ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){glout}<LEND>[call](){}<LSEP>[](symbol){utils.recalc.avgpic}<LSEP>[](symbol){glout}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){glout}<LEND>[call](){}<LSEP>[](symbol){utils.recalc.callrate}<LSEP>[](symbol){glout}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){glout}<LEND>[call](){}<LSEP>[](symbol){utils.recalc.freqhets}<LSEP>[](symbol){glout}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){glout}<LEND>[call](){}<LSEP>[](symbol){utils.recalc.freqhomref}<LSEP>[](symbol){glout}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){glout}<LEND>[call](){}<LSEP>[](symbol){utils.recalc.freqhomsnp}<LSEP>[](symbol){glout}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[litteral](logical){FALSE}<LEND>[statement 18; control flow](){if}<LSEP>[](symbol){mono.rm}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Deleting monomorphic loci (o...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){glout}<LEND>[call](){}<LSEP>[](symbol){gl.filter.monomorphs}<LSEP>[](symbol){glout}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){OneRatio}<LEND>[litteral](logical){FALSE}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){PIC}<LEND>[litteral](logical){FALSE}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nSummary of the SNP dataset\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){glout}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of individuals:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){glout}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of populations:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){glout}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){recalc}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Locus metrics provided by DA...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){mono.rm}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Monomoporhic loci not delete...}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 24; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){glout}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){print.fpcat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){mean.print}<LSEP>[](symbol){var.print}<LSEP>[](symbol){cor.print}<LSEP>[](symbol){skewness.print}<LSEP>[](symbol){kurtosis.print}<LSEP>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){group variable (observation ti...}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){variables: }<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variables}<LEND>[argument 2; litteral](str){\n\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){observation times:\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){times}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 5; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){inertia\n}<LEND>[statement 6; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){inertia}<LEND>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){...}<LEND>[statement 7; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 8; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){contributions\n}<LEND>[statement 9; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){contributions}<LEND>[](symbol){...}<LEND>[statement 10; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 11; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){qualities\n}<LEND>[statement 12; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){qualities}<LEND>[](symbol){...}<LEND>[statement 13; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 14; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){scores\n}<LEND>[statement 15; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){scores}<LEND>[](symbol){...}<LEND>[statement 16; control flow](){if}<LSEP>[](symbol){mean.print}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n.group}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){means}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){n.var}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){means}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){Means}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){means}<LEND>[](symbol){n.group}<LSEP>[](symbol){n.var}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[argument 4; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](NULL){NULL}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){mean}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variables}<LEND>[argument 2; litteral](str){.}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){Means}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){means}<LEND>[](symbol){Means}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 4; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){Means}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){contributions}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){n.var}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){st.dev}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variances}<LEND>[](symbol){diag}<LEND>[](symbol){sqrt}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){st.dev}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variances}<LEND>[](symbol){sqrt}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){Means}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){Means}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){st.dev}<LSEP>[](symbol){n.group}<LSEP>[](symbol){n.var}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[argument 4; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](NULL){NULL}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){sd}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variables}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){Means}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){Means}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){norm}<LEND>[](symbol){norm}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 8; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){means, standard deviations and...}<LEND>[statement 10; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){Means}<LSEP>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 17; control flow](){if}<LSEP>[](symbol){var.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){variances/covariances by group\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variances}<LEND>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 18; control flow](){if}<LSEP>[](symbol){cor.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){correlations by group\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){correlations}<LEND>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 19; control flow](){if}<LSEP>[](symbol){skewness.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){skewness coefficients by group\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){skewness}<LEND>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 20; control flow](){if}<LSEP>[](symbol){kurtosis.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){kurtosis coefficients by group\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){kurtosis}<LEND>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 21; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}

[](){expression}<LSEP>[litteral](NULL){NULL}<LEND>[assign](){<-}<LSEP>[](symbol){stepPattern}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){v}<LSEP>[](symbol){norm}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){obj}<LSEP>[litteral](NULL){NULL}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){v}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){obj}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){v}<LSEP>[argument 1; litteral](real){4.000000}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){v}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){obj}<LSEP>[](symbol){v}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){stepPattern constructor only s...}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){obj}<LEND>[litteral](str){stepPattern}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){obj}<LSEP>[argument 1; litteral](str){npat}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obj}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){obj}<LSEP>[argument 1; litteral](str){norm}<LEND>[](symbol){norm}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){obj}<LEND>[assign](){<-}<LSEP>[](symbol){is.stepPattern}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){stepPattern}<LEND>[assign](){<-}<LSEP>[](symbol){t.stepPattern}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tsp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tsp}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LSEP>[](symbol){tsp}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){on}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){norm}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){on}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){on}<LSEP>[argument 1; litteral](str){N}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){tsp}<LSEP>[argument 1; litteral](str){norm}<LEND>[litteral](str){M}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){on}<LSEP>[argument 1; litteral](str){M}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){tsp}<LSEP>[argument 1; litteral](str){norm}<LEND>[litteral](str){N}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){tsp}<LEND>[assign](){<-}<LSEP>[](symbol){plot.stepPattern}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pats}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xr}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){yr}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){fudge}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.500000}<LEND>[argument 1; litteral](real){1.200000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){alpha}<LSEP>[litteral](real){0.500000}<LEND>[statement 5; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 2; litteral](str){n}<LSEP>[argument 3; litteral](str){Query index}<LSEP>[argument 4; litteral](str){Reference index}<LSEP>[argument 5; litteral](real){1.000000}<LEND>[argument 6; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){yr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[argument 7; litteral](logical){FALSE}<LSEP>[](symbol){...}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){i}<LSEP>[](symbol){pats}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ss}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){i}<LEND>[statement 1; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){ss}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){ss}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 2; litteral](str){o}<LSEP>[](symbol){...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){ss}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){next}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){xh}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){alpha}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){utils}<LSEP>[](symbol){head}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){ss}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){alpha}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){ss}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){yh}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){alpha}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){utils}<LSEP>[](symbol){head}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){ss}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){alpha}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){ss}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 5; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){xh}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){yh}<LEND>[argument 2; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){ss}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){fudge}<LSEP>[](symbol){...}<LEND>[statement 7; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){xr}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](symbol){...}<LEND>[statement 8; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){yr}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](symbol){...}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){endpts}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 10; call](){}<LSEP>[](symbol){points}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){endpts}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){endpts}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 2; litteral](real){16.000000}<LSEP>[](symbol){...}<LEND>[assign](){<-}<LSEP>[](symbol){print.stepPattern}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){step.pattern}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){np}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){step.pattern}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){head}<LSEP>[litteral](str){g[i,j] = min(\n}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){body}<LSEP>[litteral](str){}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){p}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){np}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){steps}<LEND>[call](){}<LSEP>[](symbol){.extractpattern}<LSEP>[](symbol){step.pattern}<LSEP>[](symbol){p}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ns}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){steps}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){steps}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){steps}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){ns}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){s}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ns}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){di}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){steps}<LSEP>[](symbol){s}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dj}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){steps}<LSEP>[](symbol){s}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cc}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){steps}<LSEP>[](symbol){s}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dis}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){di}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){di}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){djs}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dj}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){dj}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dijs}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){i%2s,j%2s}<LSEP>[](symbol){dis}<LSEP>[](symbol){djs}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){cc}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gs}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ g[%s]}<LSEP>[](symbol){dijs}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){body}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){body}<LSEP>[](symbol){gs}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ccs}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){cc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){ }<LEND>[argument 2; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){%2.2g *}<LSEP>[](symbol){cc}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ds}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){+%s d[%s]}<LSEP>[](symbol){ccs}<LSEP>[](symbol){dijs}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){body}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){body}<LSEP>[](symbol){ds}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){body}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){body}<LSEP>[argument 1; litteral](str){,\n}<LSEP>[argument 2; litteral](str){}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tail}<LSEP>[litteral](str){)\n\n}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){norm}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){norm}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){ntxt}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){Normalization hint: %s\n}<LSEP>[](symbol){norm}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){rv}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){head}<LSEP>[](symbol){body}<LSEP>[](symbol){tail}<LSEP>[](symbol){ntxt}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Step pattern recursion:\n}<LEND>[statement 10; call](){}<LSEP>[](symbol){cat}<LSEP>[](symbol){rv}<LEND>[assign](){<-}<LSEP>[](symbol){.checkpattern}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){sp}<LEND>[body; block](){}<LEND>[assign](){<-}<LSEP>[](symbol){.mkDirDeltas}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dir}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dir}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dir}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m1}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){4.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m1}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){m1}<LEND>[assign](){<-}<LSEP>[](symbol){.extractpattern}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){sp}<LSEP>[](symbol){sn}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sbs}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sp}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){sn}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){spl}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sp}<LSEP>[](symbol){sbs}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nr}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){spl}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){spl}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){spl}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){nr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){spl}<LEND>[assign](){<-}<LSEP>[](symbol){.Pnew}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){subt}<LSEP>[](symbol){smoo}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sp}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){i}<LEND>[litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){j}<LEND>[litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){p}<LEND>[](symbol){p}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){subt}<LEND>[](symbol){subt}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){smoo}<LEND>[](symbol){smoo}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){sp}<LEND>[assign](){<-}<LSEP>[](symbol){.Pstep}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){sp}<LSEP>[](symbol){di}<LSEP>[](symbol){dj}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){i}<LEND>[](symbol){di}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){j}<LEND>[](symbol){dj}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){sp}<LEND>[assign](){<-}<LSEP>[](symbol){.Pend}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){sp}<LSEP>[](symbol){subt}<LSEP>[](symbol){smoo}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){si}<LEND>[call](){}<LSEP>[](symbol){cumsum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){sj}<LEND>[call](){}<LSEP>[](symbol){cumsum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){j}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){ni}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){si}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){si}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){nj}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){sj}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){sj}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){w}<LSEP>[litteral](NULL){NULL}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){subt}<LEND>[argument 1; litteral](str){a}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){pmin}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){j}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){subt}<LEND>[argument 1; litteral](str){b}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){pmax}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){j}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){subt}<LEND>[argument 1; litteral](str){c}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){i}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){subt}<LEND>[argument 1; litteral](str){d}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){j}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Unsupported subtype}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){smoo}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){w}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){w}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){w}<LEND>[](symbol){w}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){sp}<LEND>[assign](){<-}<LSEP>[](symbol){.PtoMx}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){sp}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nr}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mx}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){nr}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mx}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){p}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mx}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){ni}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mx}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){nj}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mx}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sp}<LSEP>[](symbol){w}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){mx}<LEND>[assign](){<-}<LSEP>[](symbol){rabinerJuangStepPattern}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){type}<LSEP>[](symbol){slope.weighting}<LSEP>[](symbol){smoothed}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sw}<LSEP>[](symbol){slope.weighting}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sm}<LSEP>[](symbol){smoothed}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){type}<LEND>[argument 1; call](){}<LSEP>[](symbol){.RJtypeI}<LSEP>[](symbol){sw}<LSEP>[](symbol){sm}<LEND>[argument 2; call](){}<LSEP>[](symbol){.RJtypeII}<LSEP>[](symbol){sw}<LSEP>[](symbol){sm}<LEND>[argument 3; call](){}<LSEP>[](symbol){.RJtypeIII}<LSEP>[](symbol){sw}<LSEP>[](symbol){sm}<LEND>[argument 4; call](){}<LSEP>[](symbol){.RJtypeIV}<LSEP>[](symbol){sw}<LSEP>[](symbol){sm}<LEND>[argument 5; call](){}<LSEP>[](symbol){.RJtypeV}<LSEP>[](symbol){sw}<LSEP>[](symbol){sm}<LEND>[argument 6; call](){}<LSEP>[](symbol){.RJtypeVI}<LSEP>[](symbol){sw}<LSEP>[](symbol){sm}<LEND>[argument 7; call](){}<LSEP>[](symbol){.RJtypeVII}<LSEP>[](symbol){sw}<LSEP>[](symbol){sm}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){norm}<LSEP>[litteral](logical){NA}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){sw}<LSEP>[argument 1; litteral](str){c}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){norm}<LSEP>[litteral](str){N}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){sw}<LSEP>[argument 1; litteral](str){d}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){norm}<LSEP>[litteral](str){N+M}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){rv}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){r}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){rs}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LSEP>[](symbol){rv}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){rs}<LSEP>[argument 1; litteral](str){norm}<LEND>[](symbol){norm}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){rs}<LSEP>[argument 1; litteral](str){call}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){rs}<LEND>[assign](){<-}<LSEP>[](symbol){.RJtypeI}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){m2}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){m3}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){m1}<LSEP>[](symbol){m2}<LSEP>[](symbol){m3}<LEND>[assign](){<-}<LSEP>[](symbol){.RJtypeII}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){m2}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){m3}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 14; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){m1}<LSEP>[](symbol){m2}<LSEP>[](symbol){m3}<LEND>[assign](){<-}<LSEP>[](symbol){.RJtypeIII}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){m2}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){m3}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){m1}<LSEP>[](symbol){m2}<LSEP>[](symbol){m3}<LEND>[assign](){<-}<LSEP>[](symbol){.RJtypeIV}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){m2}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){m3}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){m4}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 18; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){m1}<LSEP>[](symbol){m2}<LSEP>[](symbol){m3}<LSEP>[](symbol){m4}<LEND>[assign](){<-}<LSEP>[](symbol){.RJtypeV}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){m2}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){m3}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){m4}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){5.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){m5}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 26; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){m1}<LSEP>[](symbol){m2}<LSEP>[](symbol){m3}<LSEP>[](symbol){m4}<LSEP>[](symbol){m5}<LEND>[assign](){<-}<LSEP>[](symbol){.RJtypeVI}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){m2}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){m3}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 16; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){m1}<LSEP>[](symbol){m2}<LSEP>[](symbol){m3}<LEND>[assign](){<-}<LSEP>[](symbol){.RJtypeVII}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){m2}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){m3}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){m4}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){5.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){m5}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){6.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 32; assign](){<-}<LSEP>[](symbol){m6}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){7.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 34; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 35; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 36; assign](){<-}<LSEP>[](symbol){m7}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 37; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){8.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 38; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 39; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 40; assign](){<-}<LSEP>[](symbol){m8}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 41; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pnew}<LSEP>[argument 0; litteral](real){9.000000}<LSEP>[](symbol){s}<LSEP>[](symbol){m}<LEND>[statement 42; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pstep}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 43; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){.Pend}<LSEP>[](symbol){t}<LEND>[statement 44; assign](){<-}<LSEP>[](symbol){m9}<LEND>[call](){}<LSEP>[](symbol){.PtoMx}<LSEP>[](symbol){t}<LEND>[statement 45; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){m1}<LSEP>[](symbol){m2}<LSEP>[](symbol){m3}<LSEP>[](symbol){m4}<LSEP>[](symbol){m5}<LSEP>[](symbol){m6}<LSEP>[](symbol){m7}<LSEP>[](symbol){m8}<LSEP>[](symbol){m9}<LEND>[assign](){<-}<LSEP>[](symbol){symmetric1}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){1.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LSEP>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){1.000000}<LSEP>[argument 18; litteral](real){0.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){symmetric2}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){1.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LSEP>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){1.000000}<LSEP>[argument 18; litteral](real){0.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N+M}<LEND>[assign](){<-}<LSEP>[](symbol){asymmetric}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){1.000000}<LSEP>[argument 10; litteral](real){1.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LSEP>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){1.000000}<LSEP>[argument 18; litteral](real){2.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N}<LEND>[assign](){<-}<LSEP>[](symbol){.symmetricVelichkoZagoruyko}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){2.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){1.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.001000}<LEND>[argument 12; litteral](real){3.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){0.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){.asymmetricItakura}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){1.000000}<LSEP>[argument 10; litteral](real){1.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LSEP>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){2.000000}<LSEP>[argument 18; litteral](real){1.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){1.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){1.000000}<LSEP>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){0.000000}<LSEP>[argument 27; litteral](real){1.000000}<LSEP>[argument 28; litteral](real){4.000000}<LSEP>[argument 29; litteral](real){2.000000}<LSEP>[argument 30; litteral](real){2.000000}<LEND>[argument 31; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 32; litteral](real){4.000000}<LSEP>[argument 33; litteral](real){1.000000}<LSEP>[argument 34; litteral](real){0.000000}<LSEP>[argument 35; litteral](real){1.000000}<LSEP>[argument 36; litteral](real){4.000000}<LSEP>[argument 37; litteral](real){0.000000}<LSEP>[argument 38; litteral](real){0.000000}<LSEP>[argument 39; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){symmetricP0}<LSEP>[](symbol){symmetric2}<LEND>[assign](){<-}<LSEP>[](symbol){asymmetricP0}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){0.000000}<LSEP>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){1.000000}<LSEP>[argument 10; litteral](real){1.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LSEP>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){1.000000}<LSEP>[argument 18; litteral](real){0.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N}<LEND>[assign](){<-}<LSEP>[](symbol){.asymmetricP0b}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){2.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){1.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){1.000000}<LSEP>[argument 12; litteral](real){3.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){0.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N}<LEND>[assign](){<-}<LSEP>[](symbol){symmetricP05}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){2.000000}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){1.000000}<LSEP>[argument 11; litteral](real){1.000000}<LSEP>[argument 12; litteral](real){1.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LSEP>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){1.000000}<LSEP>[argument 18; litteral](real){2.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){2.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){1.000000}<LSEP>[argument 23; litteral](real){2.000000}<LSEP>[argument 24; litteral](real){2.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){0.000000}<LSEP>[argument 27; litteral](real){1.000000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){1.000000}<LSEP>[argument 30; litteral](real){1.000000}<LEND>[argument 31; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 32; litteral](real){3.000000}<LSEP>[argument 33; litteral](real){0.000000}<LSEP>[argument 34; litteral](real){0.000000}<LSEP>[argument 35; litteral](real){2.000000}<LSEP>[argument 36; litteral](real){4.000000}<LSEP>[argument 37; litteral](real){2.000000}<LSEP>[argument 38; litteral](real){1.000000}<LEND>[argument 39; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 40; litteral](real){4.000000}<LSEP>[argument 41; litteral](real){1.000000}<LSEP>[argument 42; litteral](real){0.000000}<LSEP>[argument 43; litteral](real){2.000000}<LSEP>[argument 44; litteral](real){4.000000}<LSEP>[argument 45; litteral](real){0.000000}<LSEP>[argument 46; litteral](real){0.000000}<LSEP>[argument 47; litteral](real){1.000000}<LSEP>[argument 48; litteral](real){5.000000}<LSEP>[argument 49; litteral](real){3.000000}<LSEP>[argument 50; litteral](real){1.000000}<LEND>[argument 51; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 52; litteral](real){5.000000}<LSEP>[argument 53; litteral](real){2.000000}<LSEP>[argument 54; litteral](real){0.000000}<LSEP>[argument 55; litteral](real){2.000000}<LSEP>[argument 56; litteral](real){5.000000}<LSEP>[argument 57; litteral](real){1.000000}<LSEP>[argument 58; litteral](real){0.000000}<LSEP>[argument 59; litteral](real){1.000000}<LSEP>[argument 60; litteral](real){5.000000}<LSEP>[argument 61; litteral](real){0.000000}<LSEP>[argument 62; litteral](real){0.000000}<LSEP>[argument 63; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N+M}<LEND>[assign](){<-}<LSEP>[](symbol){asymmetricP05}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){1.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 12; litteral](real){1.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){1.000000}<LSEP>[argument 18; litteral](real){2.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){2.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){1.000000}<LSEP>[argument 23; litteral](real){0.500000}<LSEP>[argument 24; litteral](real){2.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){0.000000}<LSEP>[argument 27; litteral](real){0.500000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){1.000000}<LSEP>[argument 30; litteral](real){1.000000}<LEND>[argument 31; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 32; litteral](real){3.000000}<LSEP>[argument 33; litteral](real){0.000000}<LSEP>[argument 34; litteral](real){0.000000}<LSEP>[argument 35; litteral](real){1.000000}<LSEP>[argument 36; litteral](real){4.000000}<LSEP>[argument 37; litteral](real){2.000000}<LSEP>[argument 38; litteral](real){1.000000}<LEND>[argument 39; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 40; litteral](real){4.000000}<LSEP>[argument 41; litteral](real){1.000000}<LSEP>[argument 42; litteral](real){0.000000}<LSEP>[argument 43; litteral](real){1.000000}<LSEP>[argument 44; litteral](real){4.000000}<LSEP>[argument 45; litteral](real){0.000000}<LSEP>[argument 46; litteral](real){0.000000}<LSEP>[argument 47; litteral](real){1.000000}<LSEP>[argument 48; litteral](real){5.000000}<LSEP>[argument 49; litteral](real){3.000000}<LSEP>[argument 50; litteral](real){1.000000}<LEND>[argument 51; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 52; litteral](real){5.000000}<LSEP>[argument 53; litteral](real){2.000000}<LSEP>[argument 54; litteral](real){0.000000}<LSEP>[argument 55; litteral](real){1.000000}<LSEP>[argument 56; litteral](real){5.000000}<LSEP>[argument 57; litteral](real){1.000000}<LSEP>[argument 58; litteral](real){0.000000}<LSEP>[argument 59; litteral](real){1.000000}<LSEP>[argument 60; litteral](real){5.000000}<LSEP>[argument 61; litteral](real){0.000000}<LSEP>[argument 62; litteral](real){0.000000}<LSEP>[argument 63; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N}<LEND>[assign](){<-}<LSEP>[](symbol){symmetricP1}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){1.000000}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){1.000000}<LSEP>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){1.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){2.000000}<LSEP>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){2.000000}<LSEP>[argument 22; litteral](real){1.000000}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){1.000000}<LSEP>[argument 26; litteral](real){0.000000}<LSEP>[argument 27; litteral](real){2.000000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){0.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N+M}<LEND>[assign](){<-}<LSEP>[](symbol){asymmetricP1}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){1.000000}<LSEP>[argument 7; litteral](real){0.500000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){0.500000}<LSEP>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){1.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){1.000000}<LSEP>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){2.000000}<LSEP>[argument 22; litteral](real){1.000000}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){1.000000}<LSEP>[argument 26; litteral](real){0.000000}<LSEP>[argument 27; litteral](real){1.000000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){0.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N}<LEND>[assign](){<-}<LSEP>[](symbol){symmetricP2}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){2.000000}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){1.000000}<LSEP>[argument 11; litteral](real){2.000000}<LSEP>[argument 12; litteral](real){1.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LSEP>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){1.000000}<LSEP>[argument 18; litteral](real){1.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){2.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){2.000000}<LSEP>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){3.000000}<LSEP>[argument 26; litteral](real){2.000000}<LEND>[argument 27; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){2.000000}<LSEP>[argument 30; litteral](real){1.000000}<LSEP>[argument 31; litteral](real){2.000000}<LSEP>[argument 32; litteral](real){3.000000}<LSEP>[argument 33; litteral](real){1.000000}<LSEP>[argument 34; litteral](real){0.000000}<LSEP>[argument 35; litteral](real){2.000000}<LSEP>[argument 36; litteral](real){3.000000}<LSEP>[argument 37; litteral](real){0.000000}<LSEP>[argument 38; litteral](real){0.000000}<LSEP>[argument 39; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N+M}<LEND>[assign](){<-}<LSEP>[](symbol){asymmetricP2}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){2.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){1.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 12; litteral](real){1.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){1.000000}<LSEP>[argument 18; litteral](real){1.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){2.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){1.000000}<LSEP>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){3.000000}<LSEP>[argument 26; litteral](real){2.000000}<LEND>[argument 27; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){2.000000}<LSEP>[argument 30; litteral](real){1.000000}<LSEP>[argument 31; litteral](real){1.000000}<LSEP>[argument 32; litteral](real){3.000000}<LSEP>[argument 33; litteral](real){1.000000}<LSEP>[argument 34; litteral](real){0.000000}<LSEP>[argument 35; litteral](real){1.000000}<LSEP>[argument 36; litteral](real){3.000000}<LSEP>[argument 37; litteral](real){0.000000}<LSEP>[argument 38; litteral](real){0.000000}<LSEP>[argument 39; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N}<LEND>[assign](){<-}<LSEP>[](symbol){typeIa}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){0.000000}<LSEP>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){1.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){1.000000}<LSEP>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){1.000000}<LSEP>[argument 22; litteral](real){2.000000}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){1.000000}<LSEP>[argument 27; litteral](real){1.000000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){0.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){0.000000}<LEND>[assign](){<-}<LSEP>[](symbol){typeIb}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){1.000000}<LSEP>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){1.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){1.000000}<LSEP>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){1.000000}<LSEP>[argument 22; litteral](real){2.000000}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){1.000000}<LSEP>[argument 27; litteral](real){1.000000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){0.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){typeIc}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){1.000000}<LSEP>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){1.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){1.000000}<LSEP>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){1.000000}<LSEP>[argument 22; litteral](real){2.000000}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){1.000000}<LSEP>[argument 27; litteral](real){1.000000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){0.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){0.000000}<LEND>[argument 1; litteral](str){N}<LEND>[assign](){<-}<LSEP>[](symbol){typeId}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){1.000000}<LSEP>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){1.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){2.000000}<LSEP>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){1.000000}<LSEP>[argument 22; litteral](real){2.000000}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){1.000000}<LSEP>[argument 27; litteral](real){2.000000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){0.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N+M}<LEND>[assign](){<-}<LSEP>[](symbol){typeIas}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){0.500000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){0.500000}<LSEP>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){1.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){1.000000}<LSEP>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){1.000000}<LSEP>[argument 22; litteral](real){2.000000}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){1.000000}<LSEP>[argument 27; litteral](real){0.500000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){0.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){0.500000}<LEND>[assign](){<-}<LSEP>[](symbol){typeIbs}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){1.000000}<LSEP>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){1.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){1.000000}<LSEP>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){1.000000}<LSEP>[argument 22; litteral](real){2.000000}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){1.000000}<LSEP>[argument 27; litteral](real){1.000000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){0.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){typeIcs}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){1.000000}<LSEP>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){1.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){1.000000}<LSEP>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){1.000000}<LSEP>[argument 22; litteral](real){2.000000}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){1.000000}<LSEP>[argument 27; litteral](real){0.500000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){0.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){0.500000}<LEND>[argument 1; litteral](str){N}<LEND>[assign](){<-}<LSEP>[](symbol){typeIds}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.500000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){1.500000}<LSEP>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){1.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){2.000000}<LSEP>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){1.000000}<LSEP>[argument 22; litteral](real){2.000000}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){1.000000}<LSEP>[argument 27; litteral](real){1.500000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){0.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){1.500000}<LEND>[argument 1; litteral](str){N+M}<LEND>[assign](){<-}<LSEP>[](symbol){typeIIa}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){1.000000}<LSEP>[argument 10; litteral](real){2.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LSEP>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){2.000000}<LSEP>[argument 18; litteral](real){1.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){typeIIb}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){1.000000}<LSEP>[argument 10; litteral](real){2.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){2.000000}<LSEP>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){2.000000}<LSEP>[argument 18; litteral](real){1.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){typeIIc}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){1.000000}<LSEP>[argument 10; litteral](real){2.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LSEP>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){2.000000}<LSEP>[argument 18; litteral](real){1.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){2.000000}<LEND>[argument 1; litteral](str){N}<LEND>[assign](){<-}<LSEP>[](symbol){typeIId}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){1.000000}<LSEP>[argument 10; litteral](real){2.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){3.000000}<LSEP>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){2.000000}<LSEP>[argument 18; litteral](real){1.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){3.000000}<LEND>[argument 1; litteral](str){N+M}<LEND>[assign](){<-}<LSEP>[](symbol){typeIIIc}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){1.000000}<LSEP>[argument 10; litteral](real){1.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LSEP>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){2.000000}<LSEP>[argument 18; litteral](real){1.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){1.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){1.000000}<LSEP>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){0.000000}<LSEP>[argument 27; litteral](real){1.000000}<LSEP>[argument 28; litteral](real){4.000000}<LSEP>[argument 29; litteral](real){2.000000}<LSEP>[argument 30; litteral](real){2.000000}<LEND>[argument 31; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 32; litteral](real){4.000000}<LSEP>[argument 33; litteral](real){1.000000}<LSEP>[argument 34; litteral](real){0.000000}<LSEP>[argument 35; litteral](real){1.000000}<LSEP>[argument 36; litteral](real){4.000000}<LSEP>[argument 37; litteral](real){0.000000}<LSEP>[argument 38; litteral](real){0.000000}<LSEP>[argument 39; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N}<LEND>[assign](){<-}<LSEP>[](symbol){typeIVc}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LSEP>[argument 8; litteral](real){2.000000}<LSEP>[argument 9; litteral](real){1.000000}<LSEP>[argument 10; litteral](real){2.000000}<LEND>[argument 11; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LSEP>[argument 16; litteral](real){3.000000}<LSEP>[argument 17; litteral](real){1.000000}<LSEP>[argument 18; litteral](real){3.000000}<LEND>[argument 19; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){0.000000}<LSEP>[argument 22; litteral](real){0.000000}<LSEP>[argument 23; litteral](real){1.000000}<LSEP>[argument 24; litteral](real){4.000000}<LSEP>[argument 25; litteral](real){2.000000}<LSEP>[argument 26; litteral](real){1.000000}<LEND>[argument 27; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 28; litteral](real){4.000000}<LSEP>[argument 29; litteral](real){1.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){1.000000}<LSEP>[argument 32; litteral](real){4.000000}<LSEP>[argument 33; litteral](real){0.000000}<LSEP>[argument 34; litteral](real){0.000000}<LSEP>[argument 35; litteral](real){1.000000}<LSEP>[argument 36; litteral](real){5.000000}<LSEP>[argument 37; litteral](real){2.000000}<LSEP>[argument 38; litteral](real){2.000000}<LEND>[argument 39; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 40; litteral](real){5.000000}<LSEP>[argument 41; litteral](real){1.000000}<LSEP>[argument 42; litteral](real){0.000000}<LSEP>[argument 43; litteral](real){1.000000}<LSEP>[argument 44; litteral](real){5.000000}<LSEP>[argument 45; litteral](real){0.000000}<LSEP>[argument 46; litteral](real){0.000000}<LSEP>[argument 47; litteral](real){1.000000}<LSEP>[argument 48; litteral](real){6.000000}<LSEP>[argument 49; litteral](real){2.000000}<LSEP>[argument 50; litteral](real){3.000000}<LEND>[argument 51; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 52; litteral](real){6.000000}<LSEP>[argument 53; litteral](real){1.000000}<LSEP>[argument 54; litteral](real){0.000000}<LSEP>[argument 55; litteral](real){1.000000}<LSEP>[argument 56; litteral](real){6.000000}<LSEP>[argument 57; litteral](real){0.000000}<LSEP>[argument 58; litteral](real){0.000000}<LSEP>[argument 59; litteral](real){1.000000}<LSEP>[argument 60; litteral](real){7.000000}<LSEP>[argument 61; litteral](real){3.000000}<LSEP>[argument 62; litteral](real){1.000000}<LEND>[argument 63; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 64; litteral](real){7.000000}<LSEP>[argument 65; litteral](real){2.000000}<LSEP>[argument 66; litteral](real){0.000000}<LSEP>[argument 67; litteral](real){1.000000}<LSEP>[argument 68; litteral](real){7.000000}<LSEP>[argument 69; litteral](real){1.000000}<LSEP>[argument 70; litteral](real){0.000000}<LSEP>[argument 71; litteral](real){1.000000}<LSEP>[argument 72; litteral](real){7.000000}<LSEP>[argument 73; litteral](real){0.000000}<LSEP>[argument 74; litteral](real){0.000000}<LSEP>[argument 75; litteral](real){1.000000}<LSEP>[argument 76; litteral](real){8.000000}<LSEP>[argument 77; litteral](real){3.000000}<LSEP>[argument 78; litteral](real){2.000000}<LEND>[argument 79; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 80; litteral](real){8.000000}<LSEP>[argument 81; litteral](real){2.000000}<LSEP>[argument 82; litteral](real){0.000000}<LSEP>[argument 83; litteral](real){1.000000}<LSEP>[argument 84; litteral](real){8.000000}<LSEP>[argument 85; litteral](real){1.000000}<LSEP>[argument 86; litteral](real){0.000000}<LSEP>[argument 87; litteral](real){1.000000}<LSEP>[argument 88; litteral](real){8.000000}<LSEP>[argument 89; litteral](real){0.000000}<LSEP>[argument 90; litteral](real){0.000000}<LSEP>[argument 91; litteral](real){1.000000}<LSEP>[argument 92; litteral](real){9.000000}<LSEP>[argument 93; litteral](real){3.000000}<LSEP>[argument 94; litteral](real){3.000000}<LEND>[argument 95; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 96; litteral](real){9.000000}<LSEP>[argument 97; litteral](real){2.000000}<LSEP>[argument 98; litteral](real){0.000000}<LSEP>[argument 99; litteral](real){1.000000}<LSEP>[argument 100; litteral](real){9.000000}<LSEP>[argument 101; litteral](real){1.000000}<LSEP>[argument 102; litteral](real){0.000000}<LSEP>[argument 103; litteral](real){1.000000}<LSEP>[argument 104; litteral](real){9.000000}<LSEP>[argument 105; litteral](real){0.000000}<LSEP>[argument 106; litteral](real){0.000000}<LSEP>[argument 107; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N}<LEND>[assign](){<-}<LSEP>[](symbol){mori2006}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){2.000000}<LSEP>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){0.000000}<LSEP>[argument 11; litteral](real){1.000000}<LSEP>[argument 12; litteral](real){2.000000}<LSEP>[argument 13; litteral](real){1.000000}<LSEP>[argument 14; litteral](real){1.000000}<LEND>[argument 15; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 16; litteral](real){2.000000}<LSEP>[argument 17; litteral](real){0.000000}<LSEP>[argument 18; litteral](real){0.000000}<LSEP>[argument 19; litteral](real){3.000000}<LSEP>[argument 20; litteral](real){3.000000}<LSEP>[argument 21; litteral](real){1.000000}<LSEP>[argument 22; litteral](real){2.000000}<LEND>[argument 23; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 24; litteral](real){3.000000}<LSEP>[argument 25; litteral](real){0.000000}<LSEP>[argument 26; litteral](real){1.000000}<LSEP>[argument 27; litteral](real){3.000000}<LSEP>[argument 28; litteral](real){3.000000}<LSEP>[argument 29; litteral](real){0.000000}<LSEP>[argument 30; litteral](real){0.000000}<LSEP>[argument 31; litteral](real){3.000000}<LEND>[argument 1; litteral](str){M}<LEND>[assign](){<-}<LSEP>[](symbol){rigid}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){0.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){1.000000}<LEND>[argument 1; litteral](str){N}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){logistic}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){rrreg.predictor}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){formula}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){data}<LSEP>[](symbol){rr.item}<LSEP>[](symbol){model.outcome}<LSEP>[](symbol){fit.sens}<LSEP>[](symbol){fit.outcome}<LSEP>[](symbol){bstart}<LSEP>[](symbol){tstart}<LSEP>[](symbol){parstart}<LSEP>[](symbol){maxIter}<LSEP>[](symbol){verbose}<LSEP>[](symbol){optim}<LSEP>[](symbol){em.converge}<LSEP>[](symbol){glmMaxIter}<LSEP>[](symbol){estconv}<LSEP>[](symbol){solve.tolerance}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){df.na}<LEND>[call](){}<LSEP>[](symbol){model.frame}<LSEP>[](symbol){formula}<LSEP>[](symbol){data}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df.na}<LEND>[argument 1; call](){}<LSEP>[](symbol){complete.cases}<LSEP>[](symbol){df.na}<LEND>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){xy}<LEND>[call](){}<LSEP>[](symbol){model.matrix.default}<LSEP>[](symbol){formula}<LSEP>[](symbol){df}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xy}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){xy}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){rr.item}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){bscale}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){unname}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sd}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tscale}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){bscale}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){scale}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){bscale}<LSEP>[](symbol){tscale}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){sweep}<LSEP>[](symbol){x1}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){bscale}<LSEP>[](symbol){/}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){o}<LEND>[call](){}<LSEP>[](symbol){model.response}<LSEP>[](symbol){df}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){rr.item}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){o}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){xg1}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){xg0}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){xgy}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){xgy}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){obs.llik}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){par}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){o}<LSEP>[](symbol){p}<LSEP>[](symbol){p1}<LSEP>[](symbol){xg1}<LSEP>[](symbol){xg0}<LSEP>[](symbol){fit.sens}<LSEP>[](symbol){fit.outcome}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bpar}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){par}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tpar}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){par}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){xg1}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){fx}<LEND>[call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){bpar}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){gx1}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg1}<LSEP>[](symbol){tpar}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg1}<LSEP>[](symbol){tpar}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){gx0}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg0}<LSEP>[](symbol){tpar}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg0}<LSEP>[](symbol){tpar}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){bayes}<LSEP>[litteral](real){0.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){fit.sens}<LSEP>[argument 1; litteral](str){bayesglm}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){bayes}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){bayes}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){dcauchy}<LSEP>[](symbol){tpar}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){2.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tpar}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){fit.outcome}<LSEP>[argument 1; litteral](str){bayesglm}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){bayes}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){bayes}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){dcauchy}<LSEP>[](symbol){bpar}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){2.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){bpar}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){p1}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){forceno}<LSEP>[litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){forceno}<LEND>[call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){p1}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){p1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){forceyes}<LSEP>[litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){forceyes}<LEND>[call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){p1}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){llik}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){fx}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){gx1}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[](symbol){forceno}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){fx}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){gx0}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){y}<LSEP>[](symbol){forceyes}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p1}<LEND>[](symbol){bayes}<LEND>[statement 11; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){llik}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){bstart}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){bstart}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The starting values are not th...}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){tstart}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tstart}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){xy}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The starting values are not th...}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){bstart}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bpar}<LSEP>[](symbol){bstart}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){parstart}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bpar}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rrreg}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){p}<LSEP>[](symbol){p1}<LSEP>[](symbol){p0}<LSEP>[](symbol){dat}<LSEP>[argument 5; litteral](str){forced-known}<LEND>[](symbol){est}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bpar}<LEND>[call](){}<LSEP>[](symbol){rnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){tstart}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tpar}<LSEP>[](symbol){tstart}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){parstart}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bfit}<LEND>[call](){}<LSEP>[](symbol){rrreg}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){p}<LSEP>[](symbol){p1}<LSEP>[](symbol){p0}<LSEP>[](symbol){dat}<LSEP>[argument 5; litteral](str){forced-known}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){propz}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){predict.rrreg}<LSEP>[](symbol){bfit}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](str){single}<LEND>[](symbol){est}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){predz}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){propz}<LEND>[argument 1; litteral](real){0.500000}<LEND>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){xgz}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){x}<LSEP>[](symbol){predz}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){tpar}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){glm}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){o}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){o}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){xgz}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){binomial}<LSEP>[argument 0; litteral](str){logit}<LEND>[](symbol){coef}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tpar}<LEND>[call](){}<LSEP>[](symbol){rnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){xg1}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){pllik}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){inf}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){par}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){bpar}<LSEP>[](symbol){tpar}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){llik}<LEND>[call](){}<LSEP>[](symbol){obs.llik}<LSEP>[](symbol){par}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){o}<LSEP>[](symbol){p}<LSEP>[](symbol){p1}<LSEP>[](symbol){xg1}<LSEP>[](symbol){xg0}<LSEP>[](symbol){fit.sens}<LSEP>[](symbol){fit.outcome}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){counter}<LSEP>[litteral](real){0.000000}<LEND>[statement 24; control flow](){while}<LSEP>[condition; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){counter}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){estconv}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){par}<LSEP>[](symbol){ppar}<LEND>[](symbol){em.converge}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){counter}<LSEP>[](symbol){maxIter}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){llik}<LSEP>[](symbol){pllik}<LEND>[](symbol){em.converge}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){counter}<LSEP>[](symbol){maxIter}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fx}<LEND>[call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){bpar}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){gx1}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg1}<LSEP>[](symbol){tpar}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg1}<LSEP>[](symbol){tpar}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){gx0}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg0}<LSEP>[](symbol){tpar}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg0}<LSEP>[](symbol){tpar}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){gxy}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xgy}<LSEP>[](symbol){tpar}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xgy}<LSEP>[](symbol){tpar}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){wr}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){gxy}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){fx}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){fx}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){gxy}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){fx}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){fx}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){p0}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){gx1}<LSEP>[](symbol){fx}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){gx0}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){fx}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){fit.sens}<LSEP>[argument 1; litteral](str){glm}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){zfit}<LEND>[call](){}<LSEP>[](symbol){glm}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){binomial}<LSEP>[argument 0; litteral](str){logit}<LEND>[](symbol){wr}<LEND>[argument 3; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){glmMaxIter}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){fit.sens}<LSEP>[argument 1; litteral](str){bayesglm}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){zfit}<LEND>[call](){}<LSEP>[](symbol){bayesglm}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){binomial}<LSEP>[argument 0; litteral](str){logit}<LEND>[](symbol){wr}<LEND>[argument 3; call](){}<LSEP>[](symbol){glm.control}<LSEP>[](symbol){maxIter}<LEND>[argument 4; litteral](real){2.500000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){fit.outcome}<LSEP>[argument 1; litteral](str){glm}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){vfit}<LEND>[call](){}<LSEP>[](symbol){glm}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){o}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){o}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){xgy}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){binomial}<LSEP>[argument 0; litteral](str){logit}<LEND>[](symbol){wr}<LEND>[argument 3; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){glmMaxIter}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){fit.outcome}<LSEP>[argument 1; litteral](str){bayesglm}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){vfit}<LEND>[call](){}<LSEP>[](symbol){bayesglm}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){o}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){o}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){xgy}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){binomial}<LSEP>[argument 0; litteral](str){logit}<LEND>[](symbol){wr}<LEND>[argument 3; call](){}<LSEP>[](symbol){glm.control}<LSEP>[](symbol){maxIter}<LEND>[argument 4; litteral](real){2.500000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){ppar}<LSEP>[](symbol){par}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){pllik}<LSEP>[](symbol){llik}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){bpar}<LEND>[call](){}<LSEP>[](symbol){coef}<LSEP>[](symbol){zfit}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){tpar}<LEND>[call](){}<LSEP>[](symbol){coef}<LSEP>[](symbol){vfit}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){par}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){bpar}<LSEP>[](symbol){tpar}<LEND>[statement 12; control flow](){if}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){llik}<LSEP>[](symbol){counter}<LEND>[argument 2; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){llik}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 3; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){par}<LSEP>[](symbol){counter}<LEND>[argument 2; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){par}<LSEP>[](symbol){ppar}<LEND>[argument 3; litteral](str){\n}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){llik}<LEND>[call](){}<LSEP>[](symbol){obs.llik}<LSEP>[](symbol){par}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){o}<LSEP>[](symbol){p}<LSEP>[](symbol){p1}<LSEP>[](symbol){xg1}<LSEP>[](symbol){xg0}<LSEP>[](symbol){fit.sens}<LSEP>[](symbol){fit.outcome}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){counter}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){counter}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){llik}<LSEP>[](symbol){pllik}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){llik}<LSEP>[](symbol){counter}<LEND>[argument 2; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){llik}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 3; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){par}<LSEP>[](symbol){counter}<LEND>[argument 2; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){par}<LSEP>[](symbol){ppar}<LEND>[argument 3; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){log-likelihood did not always ...}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){counter}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){maxIter}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){number of iterations exceeded ...}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){bpar}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){bpar}<LSEP>[](symbol){bscale}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){tpar}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){tpar}<LSEP>[](symbol){tscale}<LEND>[statement 27; control flow](){if}<LSEP>[](symbol){optim}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){MLEfit}<LEND>[call](){}<LSEP>[](symbol){optim}<LSEP>[](symbol){par}<LSEP>[](symbol){obs.llik}<LSEP>[argument 2; litteral](str){BFGS}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){o}<LSEP>[](symbol){xg1}<LSEP>[](symbol){xg0}<LSEP>[](symbol){p}<LSEP>[](symbol){p1}<LSEP>[](symbol){fit.sens}<LSEP>[](symbol){fit.outcome}<LSEP>[argument 12; litteral](logical){TRUE}<LEND>[argument 13; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){MLEfit}<LSEP>[](symbol){hessian}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){vcov}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){scale}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){scale}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){vcov}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){se.b}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){se}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){se.t}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){se}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){xg1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bpar.us}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){par}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tpar.us}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){par}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){xg1}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){fx}<LEND>[call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){bpar.us}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){gx1}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg1}<LSEP>[](symbol){tpar.us}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg1}<LSEP>[](symbol){tpar.us}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){gx0}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg0}<LSEP>[](symbol){tpar.us}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){o}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xg0}<LSEP>[](symbol){tpar.us}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){p1}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){forceno}<LSEP>[litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){forceno}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){p1}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){p1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){forceyes}<LSEP>[litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){forceyes}<LSEP>[](symbol){p1}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){score.rrpred}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){fx}<LSEP>[](symbol){gx1}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){p1}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){forceno}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){fx}<LEND>[](symbol){gx0}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){forceyes}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){fx}<LSEP>[](symbol){gx1}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){p1}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){forceno}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){fx}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){fx}<LEND>[](symbol){gx0}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){forceyes}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){fx}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){fx}<LSEP>[](symbol){gx1}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){p1}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){forceno}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){fx}<LEND>[](symbol){gx0}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){forceyes}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){fx}<LSEP>[](symbol){gx1}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){p1}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){forceno}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){gx1}<LEND>[](symbol){xg1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){fx}<LEND>[](symbol){gx0}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){forceyes}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){gx0}<LEND>[](symbol){xg0}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){information.rrpred}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){crossprod}<LSEP>[](symbol){score.rrpred}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){information.rrpred}<LSEP>[](symbol){solve.tolerance}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){vcov}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){scale}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){scale}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){vcov}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){se.b}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){se}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){se.t}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){se}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){xg1}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){return.object.rrreg.predictor}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){tpar}<LSEP>[](symbol){se.t}<LSEP>[](symbol){bpar}<LSEP>[](symbol){se.b}<LSEP>[](symbol){vcov}<LSEP>[](symbol){df}<LEND>[argument 6; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){rr.item}<LEND>[](symbol){x1}<LSEP>[](symbol){y}<LSEP>[](symbol){o}<LSEP>[](symbol){design}<LEND>[argument 11; call](){}<LSEP>[](symbol){match.call}<LEND>[statement 29; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){forced-known}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object.rrreg.predictor}<LSEP>[](symbol){p}<LEND>[](symbol){p}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object.rrreg.predictor}<LSEP>[](symbol){p1}<LEND>[](symbol){p1}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object.rrreg.predictor}<LSEP>[](symbol){p0}<LEND>[](symbol){p0}<LEND>[statement 30; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){mirrored}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){disguised}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object.rrreg.predictor}<LSEP>[](symbol){p}<LEND>[](symbol){p}<LEND>[statement 31; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){unrelated-known}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object.rrreg.predictor}<LSEP>[](symbol){p}<LEND>[](symbol){p}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object.rrreg.predictor}<LSEP>[](symbol){q}<LEND>[](symbol){q}<LEND>[statement 32; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){return.object.rrreg.predictor}<LEND>[litteral](str){rrreg.predictor}<LEND>[statement 33; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){return.object.rrreg.predictor}<LEND>[assign](){<-}<LSEP>[](symbol){vcov.rrreg.predictor}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){vcov}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){vcov}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coef.names}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){vcov}<LEND>[assign](){<-}<LSEP>[](symbol){coef.rrreg.predictor}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){coef}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.t}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){coef}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coef.names}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){coef}<LEND>[assign](){<-}<LSEP>[](symbol){summary.rrreg.predictor}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){structure}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){summary.rrreg.predictor}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){print.rrreg.predictor}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nRandomized Response as a Reg...}<LEND>[statement 1; call](){}<LSEP>[](symbol){dput}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){call}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){est.t}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){est.t}<LSEP>[argument 1; litteral](str){se.t}<LSEP>[argument 2; litteral](str){est.b}<LSEP>[argument 3; litteral](str){se.b}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){coef.names}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){est.t}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){se.t}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){est.b}<LEND>[argument 1; litteral](logical){NA}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){se.b}<LEND>[argument 1; litteral](logical){NA}<LEND>[statement 10; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){tb}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[statement 11; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 12; call](){}<LSEP>[](symbol){summarize.design}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){design}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p0}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p1}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){q}<LEND>[statement 13; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 14; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){print.summary.rrreg.predictor}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nRandomized Response as a Reg...}<LEND>[statement 1; call](){}<LSEP>[](symbol){dput}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){call}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){est.t}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){est.t}<LSEP>[argument 1; litteral](str){se.t}<LSEP>[argument 2; litteral](str){est.b}<LSEP>[argument 3; litteral](str){se.b}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){coef.names}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){est.t}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){se.t}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){est.b}<LEND>[argument 1; litteral](logical){NA}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){se.b}<LEND>[argument 1; litteral](logical){NA}<LEND>[statement 10; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){tb}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[statement 11; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 12; call](){}<LSEP>[](symbol){summarize.design}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){design}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p0}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p1}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){q}<LEND>[statement 13; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 14; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){predict.rrreg.predictor}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){fix.z}<LSEP>[](symbol){alpha}<LSEP>[](symbol){n.sims}<LSEP>[](symbol){avg}<LSEP>[](symbol){newdata}<LSEP>[](symbol){quasi.bayes}<LSEP>[](symbol){keep.draws}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){fix.z}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){newdata}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){propz}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p0}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.b}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.b}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.b}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p0}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xvar}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[](symbol){propz}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){newdata}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No data in the provided data f...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){covars}<LEND>[call](){}<LSEP>[](symbol){model.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.formula}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){~}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[](symbol){formula}<LEND>[argument 1; litteral](real){3.000000}<LEND>[](symbol){newdata}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newx}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){covars}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){covars}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[](symbol){rr.item}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){newy}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){covars}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){covars}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[](symbol){rr.item}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){propz}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){newy}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p0}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){newy}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p1}<LEND>[](symbol){newy}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){newx}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.b}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){newy}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){newx}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.b}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){newy}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){newx}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.b}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p1}<LEND>[](symbol){newy}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p0}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){newy}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){xvar}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){newx}<LSEP>[](symbol){propz}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fix.z}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){fix.z}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){fix.z}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fix.z must be a probability (o...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){propz}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){fix.z}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fix.z}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){fix.z}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){fix.z}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fix.z must be a probability (o...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){propz}<LSEP>[](symbol){fix.z}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fix.z must be either a single ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){newdata}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xvar}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[](symbol){propz}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){newdata}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No data in the provided data f...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){covars}<LEND>[call](){}<LSEP>[](symbol){model.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.formula}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){~}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[](symbol){formula}<LEND>[argument 1; litteral](real){3.000000}<LEND>[](symbol){newdata}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newx}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){covars}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){covars}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[](symbol){rr.item}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){xvar}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){newx}<LSEP>[](symbol){propz}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){quasi.bayes}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xvar}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.t}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){avg}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){mean}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){return.object}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){pred}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){draws}<LEND>[call](){}<LSEP>[](symbol){mvrnorm}<LSEP>[](symbol){n.sims}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.b}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.t}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){vcov}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xvar}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){draws}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.b}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.b}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est.t}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){avg}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){mean}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){est}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){mean}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){lower.ci}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){a}<LEND>[body; call](){}<LSEP>[](symbol){quantile}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){upper.ci}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){a}<LEND>[body; call](){}<LSEP>[](symbol){quantile}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){sd}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){return.object}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){est}<LSEP>[](symbol){se}<LSEP>[](symbol){lower.ci}<LSEP>[](symbol){upper.ci}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){keep.draws}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){qoi.draws}<LEND>[](symbol){pred}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){return.object}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plot.fpcat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){nscore}<LSEP>[](symbol){main}<LSEP>[](symbol){sub.title}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nscore}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Since dad-4, nscore must be a ...}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){and}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 4; litteral](str){are plotted.}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nscore}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){times}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){times}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){numtimes}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){times}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){inertia}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){inertia}<LEND>[](symbol){inertia}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){coor}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){scores}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){ngroup}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){coor}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){nscore}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){coor}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The components of nscore must ...}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){group}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){scores}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nscore}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){i1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){i2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){coorij}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){coor}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){coor}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){i1}<LSEP>[](symbol){i2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){coor}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){i1}<LSEP>[](symbol){i2}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){coorij}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){x1}<LSEP>[argument 1; litteral](str){y1}<LSEP>[argument 2; litteral](str){x2}<LSEP>[argument 3; litteral](str){y2}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){ggplot}<LSEP>[](symbol){coorij}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes_q}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){y1}<LEND>[argument 2; call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){x2}<LEND>[argument 3; call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){y2}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_segment}<LEND>[argument 0; call](){}<LSEP>[](symbol){arrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){unit}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](str){inches}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){labs}<LSEP>[](symbol){main}<LSEP>[](symbol){sub.title}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){coor}<LEND>[](symbol){i1}<LEND>[argument 1; litteral](str){ (}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){inertia}<LSEP>[](symbol){i1}<LEND>[argument 3; litteral](str){%)}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){coor}<LEND>[](symbol){i2}<LEND>[argument 1; litteral](str){ (}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){inertia}<LSEP>[](symbol){i2}<LEND>[argument 3; litteral](str){%)}<LEND>[statement 8; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){graph}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nscore}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){Date}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){times}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){times}<LEND>[call](){}<LSEP>[](symbol){as.POSIXct}<LSEP>[](symbol){times}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){ggplot}<LEND>[argument 0; call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){times}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){coor}<LSEP>[](symbol){}<LSEP>[](symbol){nscore}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes_q}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){time}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){coor}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_line}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){labs}<LSEP>[](symbol){main}<LSEP>[](symbol){sub.title}<LSEP>[argument 2; litteral](str){time}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){coor}<LEND>[](symbol){nscore}<LEND>[argument 1; litteral](str){ (}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){inertia}<LSEP>[](symbol){nscore}<LEND>[argument 3; litteral](str){%)}<LEND>[statement 5; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){graph}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.edit.recode.ind}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){out.recode.file}<LSEP>[](symbol){outpath}<LSEP>[](symbol){recalc}<LSEP>[](symbol){mono.rm}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){out.recode.file}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outfilespec}<LEND>[call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){outpath}<LSEP>[](symbol){out.recode.file}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){hold.nLoc}<LEND>[call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){hold.nInd}<LEND>[call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){hold.nPop}<LEND>[call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Extracting current individual ...}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){recode.table}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){new}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){edit}<LSEP>[](symbol){recode.table}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){new}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){out.recode.file}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){No output table specified, rec...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Writing individual recode tabl...}<LSEP>[](symbol){out.recode.file}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){write.table}<LSEP>[](symbol){new}<LSEP>[](symbol){out.recode.file}<LSEP>[argument 2; litteral](str){,}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){ind.list}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){ntr}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 18; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntr}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ind.list}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ind.list}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new}<LSEP>[](symbol){j}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Assigning new individual (=spe...}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[](symbol){ind.list}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){delete}<LEND>[argument 1; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){Delete}<LEND>[argument 1; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Deleting individuals/samples f...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.drop.ind}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Delete}<LSEP>[argument 1; litteral](str){delete}<LEND>[argument 2; litteral](real){0.000000}<LEND>[statement 22; control flow](){if}<LSEP>[](symbol){recalc}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.recalc.metrics}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 23; control flow](){if}<LSEP>[](symbol){mono.rm}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.filter.monomorphs}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n Summary of recoded dataset\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Original No. of loci:}<LSEP>[](symbol){hold.nLoc}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ New No. of loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Original No. of individuals:}<LSEP>[](symbol){hold.nInd}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ New No. of individuals:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 5; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Original No. of populations:}<LSEP>[](symbol){hold.nPop}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ New No. of populations:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n\n}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){recalc}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Note: Locus metrics not recalc...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){mono.rm}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Note: Resultant monomorphic lo...}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 28; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plot.fhclustd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){labels}<LSEP>[](symbol){hang}<LSEP>[](symbol){check}<LSEP>[](symbol){axes}<LSEP>[](symbol){frame.plot}<LSEP>[](symbol){ann}<LSEP>[](symbol){main}<LSEP>[](symbol){sub}<LSEP>[](symbol){xlab}<LSEP>[](symbol){ylab}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){clust}<LEND>[](symbol){labels}<LSEP>[](symbol){hang}<LSEP>[](symbol){check}<LSEP>[](symbol){axes}<LSEP>[](symbol){frame.plot}<LSEP>[](symbol){ann}<LSEP>[](symbol){main}<LSEP>[](symbol){sub}<LSEP>[](symbol){xlab}<LSEP>[](symbol){ylab}<LSEP>[](symbol){...}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){summary.ada}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){n.iter}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){ada}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Error: Object is not of class...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){kapstat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tab}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){tab}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){tab}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){tab}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rs}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){tab}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sum}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cs}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){tab}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){sum}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){N}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){rs}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){E}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){rs}<LSEP>[](symbol){cs}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){N}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){O}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){tab}<LEND>[](symbol){N}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){O}<LSEP>[](symbol){E}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){E}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](logical){NA}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cl}<LEND>[argument 1; litteral](real){2.000000}<LEND>[litteral](str){}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Call:\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){dput}<LSEP>[](symbol){cl}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){iter}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){iter}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){n.iter}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){n.iter}<LSEP>[](symbol){iter}<LEND>[true branch; assign](){=}<LSEP>[](symbol){iter}<LSEP>[](symbol){n.iter}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){fit}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){tab}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){confusion}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){errm}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){errs}<LEND>[](symbol){iter}<LSEP>[](symbol){}<LEND>[statement 8; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nLoss:}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){lossObj}<LEND>[](symbol){loss}<LEND>[argument 2; litteral](str){Method:}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){lossObj}<LEND>[](symbol){type}<LEND>[argument 4; litteral](str){ Iteration:}<LSEP>[](symbol){iter}<LSEP>[argument 6; litteral](str){\n}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nTraining Results\n}<LEND>[statement 10; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nAccuracy:}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){errm}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; litteral](str){Kappa:}<LEND>[argument 3; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){errm}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 4; litteral](str){\n\n}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){errm}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){l}<LSEP>[litteral](real){3.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Testing Results\n}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){k}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nAccuracy:}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){errm}<LSEP>[](symbol){l}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){l}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Kappa:}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){errm}<LSEP>[](symbol){l}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){l}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\n}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.keep.ind}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){ind.list}<LSEP>[](symbol){recalc}<LSEP>[](symbol){mono.rm}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){case}<LSEP>[](symbol){ind.list}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){case}<LEND>[argument 1; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Listed individual}<LSEP>[](symbol){case}<LSEP>[argument 2; litteral](str){not present in the dataset -- ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ind.list}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ind.list}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ind.list}<LSEP>[](symbol){case}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ind.list}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: no individuals ...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Deleteing all but the list...}<LSEP>[](symbol){ind.list}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){ind.names}<LEND>[](symbol){ind.list}<LEND>[statement 11; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 12; control flow](){if}<LSEP>[](symbol){mono.rm}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Deleting monomorphic loc\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.filter.monomorphs}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Resultant dataset m...}<LEND>[statement 14; control flow](){if}<LSEP>[](symbol){recalc}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.recalc.metrics}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Recalculating locus metrics\n}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Locus metrics not recalculat...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){utils.reset.flags}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Summary of recoded dataset\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of individuals:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of populations:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed: gl.keep.ind\n}<LEND>[statement 19; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.filter.hamming}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){threshold}<LSEP>[](symbol){rs}<LSEP>[](symbol){pb}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n0}<LEND>[call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence ...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){TrimmedSequence}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Data must include...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){threshold}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){threshold}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'threshol...}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){threshold}<LSEP>[litteral](real){0.200000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Note: Hamming distance range...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Note: Calculating pairwise H...}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){TrimmedSequence}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){TrimmedSequence}<LEND>[statement 12; assign](){=}<LSEP>[](symbol){count}<LSEP>[litteral](real){0.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){nL}<LEND>[call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){nL}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 15; control flow](){if}<LSEP>[](symbol){pb}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pbar}<LEND>[call](){}<LSEP>[](symbol){txtProgressBar}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){0.000000}<LSEP>[argument 4; litteral](str){Working ....}<LEND>[statement 1; call](){}<LSEP>[](symbol){getTxtProgressBar}<LSEP>[](symbol){pbar}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating Hamming distance...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Filtering loci with Hamming ...}<LSEP>[](symbol){threshold}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 17; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){nL}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){s1}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){TrimmedSequence}<LEND>[](symbol){i}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){nL}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){s2}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){TrimmedSequence}<LEND>[](symbol){j}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){utils.hamming}<LSEP>[](symbol){s1}<LSEP>[](symbol){s2}<LSEP>[](symbol){rs}<LEND>[](symbol){threshold}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){index}<LSEP>[](symbol){i}<LEND>[litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Deleting:}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){x}<LEND>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){x}<LEND>[](symbol){j}<LEND>[argument 3; litteral](str){\n}<LEND>[statement 2; control flow](){break}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){pb}<LEND>[true branch; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){pbar}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){nL}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){index}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){index}<LEND>[](symbol){}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n Summary of filtered dataset\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Initial No. of loci:}<LSEP>[](symbol){n0}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Hamming d >}<LSEP>[](symbol){threshold}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Loci deleted}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n0}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Final No. of loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 5; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of individuals:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of populations: }<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n\n}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 24; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}

[](){expression}<LSEP>[litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){tdTheme}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){pch}<LSEP>[](symbol){col.points}<LSEP>[](symbol){fill}<LSEP>[](symbol){cex}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){simpleTheme}<LSEP>[](symbol){pch}<LSEP>[](symbol){col.points}<LSEP>[](symbol){fill}<LSEP>[](symbol){cex}<LSEP>[](symbol){...}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){summary.RD}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Call:\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Type:\n}<LEND>[statement 5; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){type}<LEND>[argument 1; litteral](str){\n\n}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){mod}<LSEP>[litteral](logical){FALSE}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){model}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){mod}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[](symbol){model}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){mod}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[](symbol){model}<LEND>[litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[](symbol){verbose}<LEND>[litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){object}<LEND>[call](){}<LSEP>[](symbol){eval.parent}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){obs}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){n}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){type}<LEND>[argument 1; litteral](str){sharp}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){residuals}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){i}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){obs}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){residuals}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){iv}<LEND>[](symbol){i}<LEND>[statement 12; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Estimates:\n}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){stars}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[](symbol){n}<LEND>[statement 14; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stars}<LSEP>[](symbol){i}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){0.001000}<LEND>[true branch; litteral](str){***}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){0.010000}<LEND>[true branch; litteral](str){**}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){0.050000}<LEND>[true branch; litteral](str){*}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){0.100000}<LEND>[true branch; litteral](str){.}<LSEP>[false branch; litteral](str){ }<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){bw}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){obs}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){se}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){z}<LEND>[argument 5; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){n}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Bandwidth}<LSEP>[argument 1; litteral](str){Observations}<LSEP>[argument 2; litteral](str){Estimate}<LSEP>[argument 3; litteral](str){Std. Error}<LSEP>[argument 4; litteral](str){z value}<LSEP>[argument 5; litteral](str){Pr(>|z|)}<LEND>[statement 18; call](){}<LSEP>[](symbol){print.default}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){format}<LSEP>[](symbol){x}<LSEP>[](symbol){digits}<LEND>[](symbol){stars}<LEND>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 19; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){---\n}<LEND>[statement 20; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Signif. codes: 0 '***' 0.001 ...}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){out}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){out}<LEND>[litteral](str){summary.RD}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){fstat}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){n}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){type}<LEND>[argument 1; litteral](str){sharp}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fstat}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){summary}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){i}<LEND>[](symbol){fstatistic}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){summary}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){i}<LEND>[](symbol){fstatistic}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){summary}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){i}<LEND>[](symbol){fstatistic}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){pf}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){summary}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){i}<LEND>[](symbol){fstatistic}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){summary}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){i}<LEND>[](symbol){fstatistic}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){summary}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){i}<LEND>[](symbol){fstatistic}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fstat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fstat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fstat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){min}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fstat}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){summary}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){iv}<LEND>[](symbol){i}<LEND>[](symbol){waldtest}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){summary}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){iv}<LEND>[](symbol){i}<LEND>[](symbol){waldtest}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){summary}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){iv}<LEND>[](symbol){i}<LEND>[](symbol){waldtest}<LEND>[argument 1; litteral](real){4.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){summary}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){iv}<LEND>[](symbol){i}<LEND>[](symbol){waldtest}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 25; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){fstat}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){F}<LSEP>[argument 1; litteral](str){Num. DoF}<LSEP>[argument 2; litteral](str){Denom. DoF}<LSEP>[argument 3; litteral](str){p}<LEND>[statement 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){fstat}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est}<LEND>[statement 27; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){F-statistics:\n}<LEND>[statement 28; call](){}<LSEP>[](symbol){print.default}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){fstat}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){format}<LSEP>[](symbol){x}<LSEP>[](symbol){digits}<LEND>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 29; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){out}<LSEP>[](symbol){fstat}<LEND>[](symbol){fstat}<LEND>[statement 30; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){out}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){is.fdiscd.predict}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){fdiscd.predict}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){mathellingerpar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){meanL}<LSEP>[](symbol){varL}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){meanL}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){meanL}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){meanL}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){meanL}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){hellingerpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){meanL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){meanL}<LSEP>[](symbol){j}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){j}<LEND>[statement 3; call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){distances}

[](){expression}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.filter.cloneid}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){gl}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){gl}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The number of rows in the loc....}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nclones}<LEND>[call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){clone}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){nclones}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){ind}<LSEP>[litteral](logical){NA}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){clone}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nclones}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sel}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){cl}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){nclones}<LEND>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ind}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){sel}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){ind}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){ind}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){glf}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gl}<LSEP>[](symbol){}<LSEP>[](symbol){ind}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glf}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){ind}<LSEP>[](symbol){}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glf}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glf}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 11; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){glf}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.Ho}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){gl}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){gl}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){T}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){out}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){ORRRR}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){z}<LSEP>[](symbol){mu}<LSEP>[](symbol){r}<LSEP>[](symbol){initial_size}<LSEP>[](symbol){addon}<LSEP>[](symbol){method}<LSEP>[](symbol){SAAmethod}<LSEP>[](symbol){...}<LSEP>[](symbol){initial_A}<LSEP>[](symbol){initial_B}<LSEP>[](symbol){initial_D}<LSEP>[](symbol){initial_mu}<LSEP>[](symbol){initial_Sigma}<LSEP>[](symbol){ProgressBar}<LSEP>[](symbol){return_data}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LSEP>[](symbol){ProgressBar}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){requireNamespace}<LSEP>[argument 0; litteral](str){lazybar}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Package "lazybar" needed for...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){method}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){method}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){SMM}<LSEP>[argument 1; litteral](str){SAA}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Unrecognised method}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){SAA}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){SAAmethod}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){SAAmethod}<LSEP>[litteral](str){NULL}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){SAA}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){SAAmethod}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){optim}<LSEP>[argument 1; litteral](str){MM}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Unrecognised SAAmethod}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){RRRR_argument}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){RRRR_argument}<LSEP>[](symbol){itr}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){RRRR_argument}<LSEP>[](symbol){itr}<LEND>[litteral](real){10.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){RRRR_argument}<LSEP>[](symbol){earlystop}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){RRRR_argument}<LSEP>[](symbol){earlystop}<LEND>[litteral](real){0.000100}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){return_data}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){returned_data}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){z}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){returned_data}<LSEP>[litteral](NULL){NULL}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){N}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){y}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){P}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){y}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){Q}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){NCOL}<LSEP>[](symbol){initial_A}<LEND>[](symbol){r}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Mismatched dimension. The colu...}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){NCOL}<LSEP>[](symbol){initial_B}<LEND>[](symbol){r}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Mismatched dimension. The colu...}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){NROW}<LSEP>[](symbol){initial_A}<LEND>[](symbol){P}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Mismatched dimension. The row ...}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){NROW}<LSEP>[](symbol){initial_mu}<LEND>[](symbol){P}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Mismatched dimension. The row ...}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){NROW}<LSEP>[](symbol){initial_B}<LEND>[](symbol){Q}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Mismatched dimension. The row ...}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){z}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){z}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){R}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){z}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){NCOL}<LSEP>[](symbol){initial_D}<LEND>[](symbol){R}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Mismatched dimension. The colu...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){NROW}<LSEP>[](symbol){initial_D}<LEND>[](symbol){P}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Mismatched dimension. The row ...}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){mu}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){z}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){initial_D}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){initial_D}<LSEP>[](symbol){initial_mu}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){znull}<LSEP>[litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){R}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){znull}<LSEP>[litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){mu}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){N}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){initial_D}<LSEP>[](symbol){initial_mu}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){muorz}<LEND>[call](){}<LSEP>[](symbol){||}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){znull}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){z}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The numbers of realizations ar...}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){yy}<LSEP>[](symbol){y}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){xx}<LSEP>[](symbol){x}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){znull}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){zz}<LSEP>[](symbol){z}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){SMM}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){A}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){B}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){Pi}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){D}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){MM_mu}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){Sigma}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){initial_A}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){initial_B}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Pi}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 9; control flow](){if}<LSEP>[](symbol){muorz}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){D}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){initial_D}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){MM_mu}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){initial_mu}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Sigma}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){initial_Sigma}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){ybar}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){xbar}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){zbar}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){Mbar}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){SAA}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){optim}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){make_symm}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){upper.tri}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){upper.tri}<LSEP>[](symbol){m}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){para}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){muorz}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){para}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){initial_A}<LSEP>[](symbol){initial_B}<LSEP>[](symbol){initial_D}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){initial_Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){initial_Sigma}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){para}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){initial_A}<LSEP>[](symbol){initial_B}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){initial_Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){initial_Sigma}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){xk}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){wk}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){itr}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){N}<LSEP>[](symbol){initial_size}<LEND>[](symbol){addon}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){obj}<LEND>[call](){}<LSEP>[](symbol){numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){itr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){runtime}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[argument 0; litteral](str){list}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){itr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 27; control flow](){if}<LSEP>[](symbol){ProgressBar}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){pb}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){lazybar}<LSEP>[](symbol){lazyProgressBar}<LEND>[](symbol){itr}<LSEP>[argument 1; litteral](str){drift}<LEND>[statement 28; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){runtime}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){Sys.time}<LEND>[statement 29; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){itr}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){yy}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){k}<LSEP>[](symbol){initial_size}<LEND>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xx}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){k}<LSEP>[](symbol){initial_size}<LEND>[](symbol){}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LSEP>[](symbol){muorz}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){znull}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zz}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){k}<LSEP>[](symbol){initial_size}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){floor}<LSEP>[](symbol){itr}<LEND>[](symbol){itr}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){floor}<LSEP>[](symbol){itr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){yy}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){xx}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LSEP>[](symbol){muorz}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){znull}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){zz}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){yy}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){initial_size}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){addon}<LEND>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xx}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){initial_size}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){addon}<LEND>[](symbol){}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LSEP>[](symbol){muorz}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){znull}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zz}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){initial_size}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){addon}<LEND>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){N}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){y}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){SMM}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){muorz}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){temp}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Pi}<LSEP>[](symbol){k}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){D}<LSEP>[](symbol){k}<LEND>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){.}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){temp}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Pi}<LSEP>[](symbol){k}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){.}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xk}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){temp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tem}<LEND>[body; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){tem}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Sigma}<LSEP>[](symbol){k}<LEND>[](symbol){tem}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){wk}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xk}<LSEP>[](symbol){k}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dwk}<LEND>[call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){wk}<LSEP>[](symbol){k}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ybar}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){y}<LSEP>[](symbol){dwk}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xbar}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){dwk}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){muorz}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){zbar}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){z}<LSEP>[](symbol){dwk}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Mbar}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){zbar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){zbar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){zbar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){zbar}<LSEP>[](symbol){k}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){R_0}<LEND>[call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ybar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Mbar}<LSEP>[](symbol){k}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){R_1}<LEND>[call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xbar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Mbar}<LSEP>[](symbol){k}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){R_0}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ybar}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){R_1}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xbar}<LSEP>[](symbol){k}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){S_01}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){R_0}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){R_1}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){S_10}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){R_1}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){R_0}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){S_00}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){R_0}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){R_0}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){S_11}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){R_1}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){R_1}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){SSSSS}<LEND>[call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){expm}<LSEP>[](symbol){sqrtm}<LEND>[](symbol){S_11}<LEND>[](symbol){S_10}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){S_00}<LEND>[](symbol){S_01}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){expm}<LSEP>[](symbol){sqrtm}<LEND>[](symbol){S_11}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){V}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){eigen}<LSEP>[](symbol){SSSSS}<LEND>[](symbol){vectors}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){r}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){expm}<LSEP>[](symbol){sqrtm}<LEND>[](symbol){S_11}<LEND>[](symbol){V}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){S_01}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Pi}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 16; control flow](){if}<LSEP>[](symbol){muorz}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){D}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ybar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xbar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){zbar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){zbar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){zbar}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){P}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){N}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ybar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xbar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){D}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){zbar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ybar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xbar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){D}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){zbar}<LSEP>[](symbol){k}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){P}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){N}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ybar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xbar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){ybar}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xbar}<LSEP>[](symbol){k}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){obj}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Sigma}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){P}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xk}<LSEP>[](symbol){k}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){SAA}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){optim}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){muorz}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ne_log_likihood_loss}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){para}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){A}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){P}<LSEP>[](symbol){r}<LEND>[](symbol){P}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){B}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){P}<LSEP>[](symbol){r}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){P}<LEND>[](symbol){r}<LEND>[](symbol){P}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){D}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){P}<LEND>[](symbol){r}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){P}<LSEP>[](symbol){r}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){initial_D}<LEND>[](symbol){P}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){Sigma}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){P}<LSEP>[](symbol){P}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){Sigma}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){P}<LSEP>[](symbol){r}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){initial_D}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){para}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){Sigma}<LEND>[call](){}<LSEP>[](symbol){make_symm}<LSEP>[](symbol){Sigma}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){matrixcalc}<LSEP>[](symbol){is.positive.definite}<LEND>[](symbol){Sigma}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](real){inf}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){Pi}<LEND>[call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){B}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){temp}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){Pi}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){D}<LSEP>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){.}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){xk}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){temp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tem}<LEND>[body; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){tem}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){Sigma}<LEND>[](symbol){tem}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){P}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){N}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){xk}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ne_log_likihood_loss}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){para}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){A}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){P}<LSEP>[](symbol){r}<LEND>[](symbol){P}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){B}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){P}<LSEP>[](symbol){r}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){P}<LEND>[](symbol){r}<LEND>[](symbol){P}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){Sigma}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){P}<LSEP>[](symbol){P}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){Sigma}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){P}<LEND>[](symbol){r}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){para}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){Sigma}<LEND>[call](){}<LSEP>[](symbol){make_symm}<LSEP>[](symbol){Sigma}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){matrixcalc}<LSEP>[](symbol){is.positive.definite}<LEND>[](symbol){Sigma}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](real){inf}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){Pi}<LEND>[call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){B}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){temp}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){Pi}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){.}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){xk}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){temp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tem}<LEND>[body; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){tem}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){Sigma}<LEND>[](symbol){tem}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){P}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){xk}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sub_res}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stats}<LSEP>[](symbol){optim}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){para}<LSEP>[](symbol){k}<LEND>[](symbol){ne_log_likihood_loss}<LSEP>[](symbol){...}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sub_res}<LSEP>[](symbol){par}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){obj}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sub_res}<LSEP>[](symbol){value}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){znull}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sub_res}<LEND>[call](){}<LSEP>[](symbol){RRRR}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){z}<LEND>[](symbol){mu}<LSEP>[](symbol){r}<LEND>[argument 5; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LSEP>[](symbol){k}<LEND>[argument 6; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LSEP>[](symbol){k}<LEND>[argument 7; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){D}<LSEP>[](symbol){k}<LEND>[argument 8; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){MM_mu}<LSEP>[](symbol){k}<LEND>[argument 9; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Sigma}<LSEP>[](symbol){k}<LEND>[argument 10; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){RRRR_argument}<LSEP>[](symbol){itr}<LEND>[argument 11; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){RRRR_argument}<LSEP>[](symbol){earlystop}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){D}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sub_res}<LSEP>[](symbol){D}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sub_res}<LEND>[call](){}<LSEP>[](symbol){RRRR}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){x}<LEND>[](symbol){mu}<LSEP>[](symbol){r}<LEND>[argument 4; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LSEP>[](symbol){k}<LEND>[argument 5; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LSEP>[](symbol){k}<LEND>[argument 6; litteral](NULL){NULL}<LEND>[argument 7; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){MM_mu}<LSEP>[](symbol){k}<LEND>[argument 8; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Sigma}<LSEP>[](symbol){k}<LEND>[argument 9; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){RRRR_argument}<LSEP>[](symbol){itr}<LEND>[argument 10; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){RRRR_argument}<LSEP>[](symbol){earlystop}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){MM_mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sub_res}<LSEP>[](symbol){mu}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sub_res}<LSEP>[](symbol){A}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sub_res}<LSEP>[](symbol){B}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sub_res}<LSEP>[](symbol){Sigma}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){obj}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sub_res}<LSEP>[](symbol){obj}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){initial_Pi}<LEND>[call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){initial_A}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){initial_B}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){muorz}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){temp}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){initial_Pi}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){initial_D}<LSEP>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){.}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){temp}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){initial_Pi}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){.}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){xk}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){temp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tem}<LEND>[body; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){tem}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){initial_Sigma}<LEND>[](symbol){tem}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){obj}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LSEP>[](symbol){initial_Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){P}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){xk}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){initial_Pi}<LEND>[call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){initial_A}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){initial_B}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LSEP>[](symbol){mu}<LSEP>[](symbol){znull}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){temp}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){initial_Pi}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){initial_mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){.}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){znull}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){temp}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){initial_Pi}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){initial_D}<LSEP>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){.}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){temp}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){initial_Pi}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){.}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){xk}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){temp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tem}<LEND>[body; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){tem}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){initial_Sigma}<LEND>[](symbol){tem}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){obj}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LSEP>[](symbol){initial_Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){P}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){xk}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){ProgressBar}<LEND>[true branch; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pb}<LSEP>[](symbol){tick}<LEND>[](symbol){print}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){runtime}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){Sys.time}<LEND>[statement 30; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){SMM}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){muorz}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){temp}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Pi}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){D}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){.}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){temp}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Pi}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){.}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xkk}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){temp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tem}<LEND>[body; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){tem}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){tem}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){obj}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){P}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){xkk}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){SAA}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){optim}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){A}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){para}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){para}<LEND>[body; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){P}<LSEP>[](symbol){r}<LEND>[](symbol){P}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){B}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){para}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){para}<LEND>[body; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){P}<LSEP>[](symbol){r}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){P}<LEND>[](symbol){r}<LEND>[](symbol){P}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){muorz}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){D}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){para}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){para}<LEND>[body; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){P}<LEND>[](symbol){r}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){P}<LSEP>[](symbol){r}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){initial_D}<LEND>[](symbol){P}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){Sigma}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){para}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){para}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Sigma}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){P}<LSEP>[](symbol){P}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){Sigma}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){P}<LSEP>[](symbol){r}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){initial_D}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){para}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){Sigma}<LEND>[call](){}<LSEP>[](symbol){make_symm}<LSEP>[](symbol){Sigma}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){Sigma}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Sigma}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){para}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){para}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Sigma}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){P}<LSEP>[](symbol){P}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){Sigma}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){para}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){P}<LEND>[](symbol){r}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){para}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){Sigma}<LEND>[call](){}<LSEP>[](symbol){make_symm}<LSEP>[](symbol){Sigma}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){Sigma}<LEND>[statement 31; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){SAAmethod}<LSEP>[argument 1; litteral](str){MM}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){mu}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mu}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){D}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){D}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){znull}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){D}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){D}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){D}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mu}<LSEP>[litteral](NULL){NULL}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){mu}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mu}<LSEP>[](symbol){MM_mu}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mu}<LSEP>[litteral](NULL){NULL}<LEND>[statement 32; control flow](){if}<LSEP>[](symbol){znull}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){D}<LSEP>[litteral](NULL){NULL}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){history}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){mu}<LSEP>[](symbol){A}<LSEP>[](symbol){B}<LSEP>[](symbol){D}<LSEP>[](symbol){Sigma}<LSEP>[](symbol){obj}<LEND>[argument 6; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){do.call}<LEND>[argument 0; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){c}<LEND>[](symbol){runtime}<LEND>[statement 34; assign](){<-}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){method}<LSEP>[](symbol){SAAmethod}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){N}<LSEP>[](symbol){P}<LSEP>[](symbol){R}<LSEP>[](symbol){r}<LSEP>[](symbol){initial_size}<LSEP>[](symbol){addon}<LEND>[](symbol){history}<LEND>[argument 4; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){mu}<LEND>[argument 5; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){A}<LEND>[argument 6; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){B}<LEND>[argument 7; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){D}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){D}<LEND>[argument 8; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){Sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){Sigma}<LEND>[argument 9; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){obj}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){obj}<LEND>[](symbol){returned_data}<LEND>[statement 35; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){new_ORRRR}<LSEP>[](symbol){output}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){mvmStepPattern}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){elasticity}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){size}<LSEP>[](symbol){elasticity}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pn}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){size}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dx}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[](symbol){size}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dy}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){dx}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){size}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){size}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){pn}<LSEP>[](symbol){dx}<LSEP>[](symbol){dy}<LSEP>[](symbol){w}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){sp}<LEND>[call](){}<LSEP>[](symbol){stepPattern}<LSEP>[](symbol){tmp}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){sp}<LSEP>[argument 1; litteral](str){norm}<LEND>[litteral](str){N}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){sp}<LSEP>[argument 1; litteral](str){call}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){sp}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.refexchangesurl}<LSEP>[litteral](str){https://api.twelvedata.com/exc...}<LEND>[assign](){<-}<LSEP>[](symbol){ref_exchanges}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){type}<LSEP>[](symbol){as}<LSEP>[](symbol){name}<LSEP>[](symbol){code}<LSEP>[](symbol){country}<LSEP>[](symbol){apikey}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){apikey}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){apikey}<LEND>[call](){}<LSEP>[](symbol){.get_apikey}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){type}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){as}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){as}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){.refexchangesurl}<LSEP>[argument 1; litteral](str){?}<LSEP>[argument 2; litteral](str){&apikey=}<LSEP>[](symbol){apikey}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&type=}<LSEP>[](symbol){type}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){name}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&name=}<LSEP>[](symbol){name}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){code}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&code=}<LSEP>[](symbol){code}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){country}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&country=}<LSEP>[](symbol){country}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){accessed}<LEND>[call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[argument 1; litteral](str){UTC}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RcppSimdJson}<LSEP>[](symbol){fload}<LEND>[](symbol){qry}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){as}<LSEP>[argument 1; litteral](str){raw}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){qry}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){res}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[](symbol){type}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){res}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){status}<LEND>[argument 1; litteral](str){ok}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){message}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){data}<LEND>[](symbol){dat}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[argument 0; litteral](str){rbind}<LSEP>[](symbol){dat}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){dat}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The API returned NULL data.}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dat}<LSEP>[argument 1; litteral](str){accessed}<LEND>[](symbol){accessed}<LEND>[](symbol){dat}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){as.function.formula}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){args}<LEND>[call](){}<LSEP>[](symbol){deparseLhs}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){type}<LSEP>[litteral](NULL){NULL}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){args}<LEND>[call](){}<LSEP>[](symbol){getArgs}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){getType}<LSEP>[](symbol){x}<LEND>[false branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Don't know what to do with thi...}<LEND>[statement 1; call](){}<LSEP>[](symbol){addReturnType}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){aoos}<LSEP>[](symbol){makeFunDef}<LEND>[](symbol){args}<LEND>[argument 1; call](){}<LSEP>[](symbol){deparseRhs}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){environment}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){returnTypeDispatcher}<LSEP>[](symbol){type}<LEND>[assign](){<-}<LSEP>[](symbol){deparseLhs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; litteral](str){.}<LEND>[false branch; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){deparseRhs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[assign](){<-}<LSEP>[](symbol){getArgs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[](symbol){deparseLhs}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){aoos}<LSEP>[](symbol){splitTrim}<LEND>[](symbol){lhs}<LSEP>[argument 1; litteral](str){:}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){\\(}<LSEP>[](symbol){lhs}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){aoos}<LSEP>[](symbol){deleteBeforeParan}<LEND>[](symbol){lhs}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lhs}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){aoos}<LSEP>[](symbol){deleteEnclosingParan}<LEND>[](symbol){lhs}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){aoos}<LSEP>[](symbol){splitTrim}<LEND>[](symbol){lhs}<LSEP>[argument 1; litteral](str){,}<LEND>[false branch; block](){}<LSEP>[](symbol){lhs}<LEND>[assign](){<-}<LSEP>[](symbol){getType}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){deparseLhs}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){:::}<LSEP>[](symbol){aoos}<LSEP>[](symbol){splitTrim}<LEND>[](symbol){type}<LSEP>[argument 1; litteral](str){:}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){type}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; litteral](NULL){NULL}<LEND>[false branch; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){%g%}<LEND>[argument 0; call](){}<LSEP>[](symbol){returnTypeDispatcher}<LSEP>[](symbol){x}<LEND>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){%m%}<LEND>[argument 0; call](){}<LSEP>[](symbol){returnTypeDispatcher}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){x}<LSEP>[](symbol){character}<LEND>[argument 1; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){\\(}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){ReturnPrototype}<LSEP>[](symbol){x}<LEND>[false branch; call](){}<LSEP>[](symbol){ReturnType}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){=}<LSEP>[](symbol){kConstantSLP}<LSEP>[litteral](real){1013.250000}<LEND>[assign](){=}<LSEP>[](symbol){kConstantP0}<LSEP>[litteral](real){1000.000000}<LEND>[assign](){=}<LSEP>[](symbol){kConstantSpeedOfLight}<LSEP>[litteral](real){300000000.000000}<LEND>[assign](){=}<LSEP>[](symbol){kConstantRe}<LSEP>[litteral](real){6374000.000000}<LEND>[assign](){=}<LSEP>[](symbol){kConstantR43}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){kConstantRe}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](real){3.000000}<LEND>[assign](){=}<LSEP>[](symbol){kConstantBoltz}<LSEP>[litteral](real){0.000000}<LEND>[assign](){<-}<LSEP>[](symbol){AttenuationAbsCoeff}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){D}<LSEP>[](symbol){lam}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Km}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){pi}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){D}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[](symbol){lam}<LEND>[argument 1; call](){}<LSEP>[](symbol){Im}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){Km}<LEND>[assign](){<-}<LSEP>[](symbol){AttenuationScatCoeff}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){D}<LSEP>[](symbol){lam}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){Km}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){pi}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){D}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){lam}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){Km}<LEND>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){AttenuationExtCoeff}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){D}<LSEP>[](symbol){lam}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Qa}<LEND>[call](){}<LSEP>[](symbol){AttenuationAbsCoeff}<LSEP>[](symbol){D}<LSEP>[](symbol){lam}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){Qs}<LEND>[call](){}<LSEP>[](symbol){AttenuationScatCoeff}<LSEP>[](symbol){D}<LSEP>[](symbol){lam}<LSEP>[](symbol){m}<LEND>[statement 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){Qa}<LSEP>[](symbol){Qs}<LEND>[assign](){<-}<LSEP>[](symbol){ConversiondBZ2Z}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dBZ}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){dBZ}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[assign](){<-}<LSEP>[](symbol){ConversionZ2dBZ}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Zlin}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log10}<LSEP>[](symbol){Zlin}<LEND>[assign](){<-}<LSEP>[](symbol){DopplerFreq}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){lam}<LSEP>[](symbol){speedOfLight}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){speedOfLight}<LSEP>[](symbol){lam}<LEND>[assign](){<-}<LSEP>[](symbol){DopplerWavelength}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){freq}<LSEP>[](symbol){speedOfLight}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){speedOfLight}<LSEP>[](symbol){freq}<LEND>[assign](){<-}<LSEP>[](symbol){DopplerPulseDuration}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tau}<LSEP>[](symbol){speedOfLight}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){tau}<LEND>[](symbol){speedOfLight}<LEND>[assign](){<-}<LSEP>[](symbol){DopplerPulseLength}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){pDur}<LSEP>[](symbol){speedOfLight}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){speedOfLight}<LSEP>[](symbol){pDur}<LEND>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){DopplerFmax}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){PRF}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){PRF}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){DopplerVmax}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){PRF}<LSEP>[](symbol){lam}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){PRF}<LSEP>[](symbol){lam}<LEND>[argument 1; litteral](real){4.000000}<LEND>[assign](){<-}<LSEP>[](symbol){DopplerRmax}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){PRF}<LSEP>[](symbol){speedOfLight}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){speedOfLight}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){PRF}<LEND>[assign](){<-}<LSEP>[](symbol){DopplerDilemma}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){inFloat}<LSEP>[](symbol){lam}<LSEP>[](symbol){speedOfLight}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){speedOfLight}<LSEP>[](symbol){lam}<LEND>[argument 1; litteral](real){8.000000}<LEND>[](symbol){inFloat}<LEND>[assign](){<-}<LSEP>[](symbol){DopplerVshift}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){GS}<LSEP>[](symbol){psi}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){GS}<LEND>[argument 1; call](){}<LSEP>[](symbol){cos}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[argument 1; litteral](real){360.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){psi}<LEND>[assign](){<-}<LSEP>[](symbol){DopplerVmaxDual}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){lam}<LSEP>[](symbol){PRF1}<LSEP>[](symbol){PRF2}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){lam}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){PRF1}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){PRF2}<LEND>[assign](){<-}<LSEP>[](symbol){GeometryReffective}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dNdH}<LSEP>[](symbol){earthRadius}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){earthRadius}<LSEP>[argument 1; litteral](real){1000.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){dNdH}<LEND>[argument 1; litteral](real){1000.000000}<LEND>[assign](){<-}<LSEP>[](symbol){GeometryHalfPowerRadius}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LSEP>[](symbol){bwhalf}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LSEP>[](symbol){pi}<LEND>[argument 1; litteral](real){360.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){bwhalf}<LEND>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){GeometryRayHeight}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LSEP>[](symbol){elev}<LSEP>[](symbol){H0}<LSEP>[](symbol){R1}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){Term1}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){R1}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){r}<LEND>[](symbol){R1}<LEND>[argument 1; call](){}<LSEP>[](symbol){sin}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[argument 1; litteral](real){360.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){elev}<LEND>[statement 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){Term1}<LSEP>[](symbol){R1}<LEND>[](symbol){H0}<LEND>[assign](){<-}<LSEP>[](symbol){GeometrySampleVolIdeal}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LSEP>[](symbol){bwH}<LSEP>[](symbol){bwV}<LSEP>[](symbol){pLength}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){pi}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LSEP>[](symbol){pi}<LEND>[argument 1; litteral](real){360.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){bwH}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LSEP>[](symbol){pi}<LEND>[argument 1; litteral](real){360.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){bwV}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pLength}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){GeometrySampleVolGauss}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LSEP>[](symbol){bwH}<LSEP>[](symbol){bwV}<LSEP>[](symbol){pLength}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){Numer}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){pi}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){pi}<LEND>[argument 1; litteral](real){360.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){bwH}<LEND>[](symbol){pi}<LEND>[argument 1; litteral](real){360.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){bwV}<LEND>[](symbol){pLength}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){Denom}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){16.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){Numer}<LSEP>[](symbol){Denom}<LEND>[assign](){<-}<LSEP>[](symbol){GeometryRangeCorrect}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LSEP>[](symbol){h}<LSEP>[](symbol){E}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){h}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){dh1}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){h}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){h}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){dh2}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){h}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){dh1}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){a90r}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){dr}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){dh2}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){tan}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){a90r}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[argument 1; litteral](real){360.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){E}<LEND>[statement 5; call](){}<LSEP>[](symbol){cumsum}<LSEP>[](symbol){dr}<LEND>[assign](){<-}<LSEP>[](symbol){GeometryBeamBlockFrac}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Th}<LSEP>[](symbol){Bh}<LSEP>[](symbol){a}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){Th}<LSEP>[](symbol){Bh}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){Numer}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){asin}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){y}<LSEP>[](symbol){a}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){pi}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){Denom}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){pi}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){Numer}<LSEP>[](symbol){Denom}<LEND>[assign](){<-}<LSEP>[](symbol){SystemGainPratio}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){P1}<LSEP>[](symbol){P2}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log10}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){P1}<LSEP>[](symbol){P2}<LEND>[assign](){<-}<LSEP>[](symbol){SystemFreq}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){lam}<LSEP>[](symbol){speedOfLight}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){speedOfLight}<LSEP>[](symbol){lam}<LEND>[assign](){<-}<LSEP>[](symbol){Systemwavelength}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){freq}<LSEP>[](symbol){speedOfLight}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){speedOfLight}<LSEP>[](symbol){freq}<LEND>[assign](){<-}<LSEP>[](symbol){SystemRadarConst}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Pt}<LSEP>[](symbol){G}<LSEP>[](symbol){Tau}<LSEP>[](symbol){lam}<LSEP>[](symbol){bwH}<LSEP>[](symbol){bwV}<LSEP>[](symbol){Lm}<LSEP>[](symbol){Lr}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){Lmlin}<LEND>[call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){Lm}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){Lrlin}<LEND>[call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){Lr}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){Glin}<LEND>[call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){G}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){bwHr}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[argument 1; litteral](real){360.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){bwH}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){bwVr}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[argument 1; litteral](real){360.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){bwV}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){Numer}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){pi}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[](symbol){c}<LEND>[](symbol){Pt}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){Glin}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){Tau}<LEND>[](symbol){bwHr}<LEND>[](symbol){bwVr}<LEND>[](symbol){Lmlin}<LEND>[](symbol){Lrlin}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){Denom}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){1024.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){lam}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 7; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){Numer}<LSEP>[](symbol){Denom}<LEND>[assign](){<-}<LSEP>[](symbol){SystemAntEffArea}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){G}<LSEP>[](symbol){lam}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){Glin}<LEND>[call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){G}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Glin}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){lam}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){pi}<LEND>[assign](){<-}<LSEP>[](symbol){SystemPowerTarget}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Pt}<LSEP>[](symbol){G}<LSEP>[](symbol){Asig}<LSEP>[](symbol){r}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){Glin}<LEND>[call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){G}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Pt}<LSEP>[](symbol){Glin}<LEND>[](symbol){Asig}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){pi}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){SystemXsecBscatterSphere}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){D}<LSEP>[](symbol){lam}<LSEP>[](symbol){K}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){pi}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){K}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){D}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){lam}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[assign](){<-}<LSEP>[](symbol){SystemNormXsecBscatterSphere}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){D}<LSEP>[](symbol){lam}<LSEP>[](symbol){K}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){sig}<LEND>[call](){}<LSEP>[](symbol){SystemXsecBscatterSphere}<LSEP>[](symbol){D}<LSEP>[](symbol){lam}<LSEP>[](symbol){K}<LEND>[statement 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sig}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){pi}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){D}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){SystemSizeParam}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){D}<LSEP>[](symbol){lam}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){pi}<LEND>[](symbol){D}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){lam}<LEND>[assign](){<-}<LSEP>[](symbol){SystemPowerReturnTarget}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Pt}<LSEP>[](symbol){G}<LSEP>[](symbol){lam}<LSEP>[](symbol){sig}<LSEP>[](symbol){r}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){Glin}<LEND>[call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){G}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Pt}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){Glin}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){lam}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){sig}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){64.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){pi}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[assign](){<-}<LSEP>[](symbol){SystemThermalNoise}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Bn}<LSEP>[](symbol){Units}<LSEP>[](symbol){Ts}<LSEP>[](symbol){k}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){N}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){k}<LSEP>[](symbol){Ts}<LEND>[](symbol){Bn}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){toupper}<LSEP>[](symbol){Units}<LEND>[argument 1; litteral](str){W}<LEND>[true branch; assign](){=}<LSEP>[](symbol){Nt}<LSEP>[](symbol){N}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){toupper}<LSEP>[](symbol){Units}<LEND>[argument 1; litteral](str){DBM}<LEND>[true branch; assign](){=}<LSEP>[](symbol){Nt}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log10}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){3.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Units must be in 'W' or 'dBm'}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){Nt}<LSEP>[litteral](logical){NA}<LEND>[](symbol){Nt}<LEND>[assign](){<-}<LSEP>[](symbol){VariablesReflectivity}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Pt}<LSEP>[](symbol){G}<LSEP>[](symbol){Tau}<LSEP>[](symbol){lam}<LSEP>[](symbol){bwH}<LSEP>[](symbol){bwV}<LSEP>[](symbol){Lm}<LSEP>[](symbol){Lr}<LSEP>[](symbol){Pr}<LSEP>[](symbol){r}<LSEP>[](symbol){K}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){C1}<LEND>[call](){}<LSEP>[](symbol){SystemRadarConst}<LSEP>[](symbol){Pt}<LSEP>[](symbol){G}<LSEP>[](symbol){Tau}<LSEP>[](symbol){lam}<LSEP>[](symbol){bwH}<LSEP>[](symbol){bwV}<LSEP>[](symbol){Lm}<LSEP>[](symbol){Lr}<LEND>[statement 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){Pr}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){C1}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){K}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){VariablesRadVel}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){f}<LSEP>[](symbol){lam}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){f}<LSEP>[](symbol){lam}<LEND>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){VariablesCDR}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Zpar}<LSEP>[](symbol){Zorth}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log10}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){Zpar}<LSEP>[](symbol){Zorth}<LEND>[assign](){<-}<LSEP>[](symbol){VariablesLDR}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Zh}<LSEP>[](symbol){Zv}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log10}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){Zh}<LSEP>[](symbol){Zv}<LEND>[assign](){<-}<LSEP>[](symbol){VariablesZDR}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Zh}<LSEP>[](symbol){Zv}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log10}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){Zh}<LSEP>[](symbol){Zv}<LEND>[assign](){<-}<LSEP>[](symbol){VariablesZDP}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Zh}<LSEP>[](symbol){Zv}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){Zh}<LSEP>[](symbol){Zv}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){ZDP}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log10}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){Zh}<LSEP>[](symbol){Zv}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Zh < Zv !}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){ZDP}<LSEP>[litteral](logical){NA}<LEND>[](symbol){ZDP}<LEND>[assign](){<-}<LSEP>[](symbol){VariablesHDR}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dBZh}<LSEP>[](symbol){ZDR}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){ZDR}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; assign](){=}<LSEP>[](symbol){f}<LSEP>[litteral](real){27.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){ZDR}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){ZDR}<LSEP>[argument 1; litteral](real){1.740000}<LEND>[true branch; assign](){=}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){19.000000}<LSEP>[](symbol){ZDR}<LEND>[argument 1; litteral](real){27.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){ZDR}<LSEP>[argument 1; litteral](real){1.740000}<LEND>[true branch; assign](){=}<LSEP>[](symbol){f}<LSEP>[litteral](real){60.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){dBZh}<LSEP>[](symbol){f}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.make.recode.pop}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){out.recode.file}<LSEP>[](symbol){outpath}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){outfilespec}<LEND>[call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){outpath}<LSEP>[](symbol){out.recode.file}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: Population name...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Creating draft lookup table\n}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Writing draft lookup table to}<LSEP>[](symbol){outfilespec}<LSEP>[argument 2; litteral](str){. Edit before use\n}<LEND>[statement 12; call](){}<LSEP>[](symbol){write.table}<LSEP>[](symbol){mat}<LSEP>[](symbol){outfilespec}<LSEP>[argument 2; litteral](str){,}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 14; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){utils.outflank.plotter}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){withOutliers}<LSEP>[](symbol){NoCorr}<LSEP>[](symbol){Hmin}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){Zoom}<LSEP>[](symbol){RightZoomFraction}<LSEP>[](symbol){titletext}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){results}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){results}<LEND>[](symbol){He}<LEND>[](symbol){Hmin}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){NoCorr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){FSTNoCorr}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){fbar}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){T1NoCorr}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){T2NoCorr}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){titletext}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){titletext}<LSEP>[argument 1; litteral](str){Fst without sample size correc...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){NoCorr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){FST}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){fbar}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){FSTbar}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){titletext}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){titletext}<LSEP>[argument 1; litteral](str){Fst with sample size correction}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){flist}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){flist}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){keeperlist}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){OutlierFlag}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){withOutliers}<LEND>[true branch; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){flist}<LSEP>[](symbol){keeperlist}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){Zoom}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){FstDistPlotterZoom}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){dfInferred}<LEND>[](symbol){flist}<LSEP>[](symbol){fbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){titletext}<LSEP>[](symbol){RightZoomFraction}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){FstDistPlotter}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){dfInferred}<LEND>[](symbol){flist}<LSEP>[](symbol){fbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){titletext}<LEND>[assign](){=}<LSEP>[](symbol){FstDistPlotter}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){df}<LSEP>[](symbol){FSTlist}<LSEP>[](symbol){FSTbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){titletext}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){xPlotUpperBound}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){FSTlist}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){breakslist}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xPlotUpperBound}<LSEP>[](symbol){binwidth}<LEND>[](symbol){binwidth}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){breaks}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){breakslist}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){x}<LSEP>[](symbol){breakslist}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){breaks}<LEND>[body; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){FSTlist}<LEND>[](symbol){y}<LEND>[statement 7; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){FSTlist}<LSEP>[argument 1; litteral](str){darkgoldenrod1}<LSEP>[](symbol){breakslist}<LSEP>[](symbol){F}<LSEP>[argument 4; litteral](str){Fst}<LSEP>[](symbol){titletext}<LEND>[statement 8; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[argument 2; litteral](str){darkblue}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[assign](){=}<LSEP>[](symbol){FstDistPlotterZoom}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){df}<LSEP>[](symbol){FSTlist}<LSEP>[](symbol){FSTbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){titletext}<LSEP>[](symbol){RightZoomFraction}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){FSTlistNoNA}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){FSTlist}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){FSTlist}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){xPlotUpperBound}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){FSTlistNoNA}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){xPlotLowerBound}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stats}<LSEP>[](symbol){quantile}<LEND>[](symbol){FSTlistNoNA}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){RightZoomFraction}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){FSTlistNoNA}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){FSTlistNoNA}<LSEP>[](symbol){xPlotLowerBound}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){breakslist}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){xPlotLowerBound}<LSEP>[](symbol){xPlotUpperBound}<LSEP>[](symbol){binwidth}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){breaks}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){breakslist}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){x}<LSEP>[](symbol){breakslist}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 8; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){breaks}<LEND>[body; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xPlotLowerBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xPlotLowerBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){FSTlistNoNA}<LEND>[](symbol){y}<LEND>[statement 10; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){flist}<LSEP>[argument 1; litteral](str){darkgoldenrod1}<LSEP>[](symbol){breakslist}<LSEP>[](symbol){F}<LSEP>[argument 4; litteral](str){Fst}<LSEP>[](symbol){titletext}<LEND>[statement 11; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[argument 2; litteral](str){darkblue}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[assign](){=}<LSEP>[](symbol){FstDistPlotterAddBadCurve}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){df}<LSEP>[](symbol){FSTlist}<LSEP>[](symbol){FSTbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){RightZoomFraction}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){FSTlistNoNA}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){FSTlist}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){FSTlist}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){xPlotUpperBound}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){FSTlistNoNA}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){xPlotLowerBound}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stats}<LSEP>[](symbol){quantile}<LEND>[](symbol){FSTlistNoNA}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){RightZoomFraction}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){breakslist}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){xPlotLowerBound}<LSEP>[](symbol){xPlotUpperBound}<LSEP>[](symbol){binwidth}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){breaks}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){breakslist}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){x}<LSEP>[](symbol){breakslist}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){breaks}<LEND>[body; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xPlotLowerBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xPlotLowerBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[statement 8; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){FSTlistNoNA}<LEND>[](symbol){y}<LEND>[statement 9; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[argument 2; litteral](str){red}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[assign](){=}<LSEP>[](symbol){OutFLANKBadCurvePlotter}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){badDF}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){withOutliers}<LSEP>[](symbol){NoCorr}<LSEP>[](symbol){Hmin}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){Zoom}<LSEP>[](symbol){RightZoomFraction}<LSEP>[](symbol){titletext}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){results}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){results}<LEND>[](symbol){He}<LEND>[](symbol){Hmin}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){NoCorr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){FSTNoCorr}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){fbar}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){T1NoCorr}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){T2NoCorr}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){NoCorr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){FST}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){fbar}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){FSTbar}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){flist}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){flist}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){keeperlist}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){OutlierFlag}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){withOutliers}<LEND>[true branch; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){flist}<LSEP>[](symbol){keeperlist}<LEND>[statement 6; call](){}<LSEP>[](symbol){FstDistPlotterAddBadCurve}<LSEP>[](symbol){badDF}<LSEP>[](symbol){flist}<LSEP>[](symbol){fbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){RightZoomFraction}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){projectRasterDWD}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LSEP>[](symbol){proj}<LSEP>[](symbol){extent}<LSEP>[](symbol){adjust05}<LSEP>[](symbol){targetproj}<LSEP>[](symbol){quiet}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){checkSuggestedPackage}<LSEP>[argument 0; litteral](str){raster}<LSEP>[argument 1; litteral](str){rdwd::projectRasterDWD}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){starttime}<LEND>[call](){}<LSEP>[](symbol){Sys.time}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){proj}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p_radolan}<LSEP>[litteral](str){+proj=stere +lat_0=90 +lat_ts=...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){p_seasonal}<LSEP>[litteral](str){+proj=tmerc +lat_0=0 +lon_0=9 ...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){p_nc}<LSEP>[litteral](str){+init=epsg:3034}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){proj}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){proj}<LEND>[call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){proj}<LSEP>[](symbol){p_radolan}<LSEP>[](symbol){p_seasonal}<LSEP>[](symbol){p_nc}<LSEP>[](symbol){proj}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){proj}<LSEP>[argument 1; litteral](str){CRS}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){proj}<LEND>[call](){}<LSEP>[](symbol){suppressWarnings}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){sp}<LSEP>[](symbol){CRS}<LEND>[](symbol){proj}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){e_radolan}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){523.462200}<LEND>[argument 1; litteral](real){376.537800}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){4658.645000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){3758.645000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){e_rw}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){443.462200}<LEND>[argument 1; litteral](real){456.537800}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){4758.645000}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){3658.645000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){e_seasonal}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){3280414.711633}<LSEP>[argument 1; litteral](real){3934414.711633}<LSEP>[argument 2; litteral](real){5237500.628906}<LSEP>[argument 3; litteral](real){6103500.628906}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){e_nc}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){3667000.000000}<LSEP>[argument 1; litteral](real){4389000.000000}<LSEP>[argument 2; litteral](real){2242000.000000}<LSEP>[argument 3; litteral](real){3181000.000000}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){extent}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){extent}<LEND>[call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){extent}<LSEP>[](symbol){e_radolan}<LSEP>[](symbol){e_rw}<LSEP>[](symbol){e_seasonal}<LSEP>[](symbol){e_nc}<LEND>[statement 10; control flow](){if}<LSEP>[](symbol){adjust05}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){extent}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){extent}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Setting raster projection to }<LSEP>[](symbol){proj}<LSEP>[argument 2; litteral](str){ ...}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){projection}<LEND>[](symbol){r}<LEND>[](symbol){proj}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Setting raster extent to }<LEND>[argument 1; call](){}<LSEP>[](symbol){toString}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){extent}<LSEP>[](symbol){I}<LEND>[argument 2; litteral](str){ ...}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){extent}<LEND>[](symbol){r}<LEND>[](symbol){extent}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){targetproj}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){targetproj}<LEND>[true branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){targetproj}<LSEP>[argument 1; litteral](str){ll}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){targetproj}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){sp}<LSEP>[](symbol){CRS}<LEND>[argument 0; litteral](str){+proj=longlat +datum=WGS84 +no...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Reprojecting raster to }<LSEP>[](symbol){targetproj}<LSEP>[argument 2; litteral](str){ ...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rtitle}<LEND>[call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){r}<LSEP>[](symbol){title}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){suppressWarnings}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){projectRaster}<LEND>[](symbol){r}<LSEP>[](symbol){targetproj}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){r}<LSEP>[](symbol){title}<LEND>[](symbol){rtitle}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){dt}<LEND>[call](){}<LSEP>[](symbol){difftime}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[](symbol){starttime}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){projectRasterDWD took }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){dt}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){ }<LEND>[argument 3; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dt}<LSEP>[argument 1; litteral](str){units}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){r}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){is.fixed}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){s1}<LSEP>[](symbol){s2}<LSEP>[](symbol){tloc}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){s1}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){s2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){result}<LSEP>[litteral](logical){NA}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){s1}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){tloc}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){s1}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){s1}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){tloc}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){s1}<LSEP>[litteral](real){100.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){s2}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){tloc}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){s2}<LSEP>[litteral](real){0.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){s2}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){tloc}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){s2}<LSEP>[litteral](real){100.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){result}<LSEP>[litteral](real){0.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){s1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){s2}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){result}<LSEP>[litteral](real){1.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){s1}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){s2}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){result}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){result}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){runLocalTests}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dir_data}<LSEP>[](symbol){dir_exmpl}<LSEP>[](symbol){fast}<LSEP>[](symbol){devcheck}<LSEP>[](symbol){radar}<LSEP>[](symbol){all_Potsdam_files}<LSEP>[](symbol){index}<LSEP>[](symbol){indexfast}<LSEP>[](symbol){examples}<LSEP>[](symbol){quiet}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){checkSuggestedPackage}<LSEP>[argument 0; litteral](str){testthat}<LSEP>[argument 1; litteral](str){runLocalTests}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){rdwd$}<LEND>[argument 1; call](){}<LSEP>[](symbol){getwd}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){getwd must be in package root ...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){begintime}<LEND>[call](){}<LSEP>[](symbol){Sys.time}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){messaget}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){ (}<LEND>[argument 2; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){difftime}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[](symbol){begintime}<LSEP>[argument 2; litteral](str){s}<LEND>[argument 3; litteral](str){ secs so far)}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){dir_exmpl}<LSEP>[argument 1; litteral](str){/warnings.txt}<LEND>[statement 5; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){++ Testing dataDWD + readDWD.data}<LEND>[statement 6; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){dataDWD works}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){link}<LEND>[call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){Potsdam}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){recent}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){file}<LEND>[call](){}<LSEP>[](symbol){dataDWD}<LSEP>[](symbol){link}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[](symbol){dir_data}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){basename}<LSEP>[](symbol){file}<LEND>[argument 1; litteral](str){daily_kl_recent_tageswerte_KL_...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){links}<LEND>[call](){}<LSEP>[](symbol){selectDWD}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){5302.000000}<LSEP>[argument 1; litteral](real){5711.000000}<LSEP>[argument 2; litteral](real){3987.000000}<LEND>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){more_precip}<LSEP>[argument 3; litteral](str){h}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_error}<LEND>[argument 0; call](){}<LSEP>[](symbol){dataDWD}<LSEP>[](symbol){links}<LSEP>[](symbol){dir_data}<LEND>[argument 1; litteral](str){url must be a vector, not a list}<LEND>[statement 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){dataDWD}<LSEP>[argument 0; litteral](str){multi/mean/Temp.txt}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](str){dataDWD needs urls starting wi...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){dwdbase}<LSEP>[argument 1; litteral](str){/daily/kl/historical/tageswert...}<LEND>[statement 7; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){dataDWD}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](str){If files have been renamed on ...}<LEND>[statement 8; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){dataDWD}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){multi/mean/Temp.txt}<LSEP>[](symbol){f}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](str){urls starting with .* renamed ...}<LEND>[statement 7; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){readDWD.data works for regular...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){link}<LEND>[call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){Potsdam}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){recent}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){file}<LEND>[call](){}<LSEP>[](symbol){dataDWD}<LSEP>[](symbol){link}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[](symbol){dir_data}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){clim}<LEND>[call](){}<LSEP>[](symbol){readDWD}<LSEP>[](symbol){file}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){supposedcolnames}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){STATIONS_ID}<LSEP>[argument 1; litteral](str){MESS_DATUM}<LSEP>[argument 2; litteral](str){QN_3}<LSEP>[argument 3; litteral](str){FX}<LSEP>[argument 4; litteral](str){FM}<LSEP>[argument 5; litteral](str){QN_4}<LSEP>[argument 6; litteral](str){RSK}<LSEP>[argument 7; litteral](str){RSKF}<LSEP>[argument 8; litteral](str){SDK}<LSEP>[argument 9; litteral](str){SHK_TAG}<LSEP>[argument 10; litteral](str){NM}<LSEP>[argument 11; litteral](str){VPM}<LSEP>[argument 12; litteral](str){PM}<LSEP>[argument 13; litteral](str){TMK}<LSEP>[argument 14; litteral](str){UPM}<LSEP>[argument 15; litteral](str){TXK}<LSEP>[argument 16; litteral](str){TNK}<LSEP>[argument 17; litteral](str){TGK}<LSEP>[argument 18; litteral](str){eor}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){clim}<LEND>[](symbol){supposedcolnames}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){climf}<LEND>[call](){}<LSEP>[](symbol){readDWD}<LSEP>[](symbol){file}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 6; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[](symbol){clim}<LSEP>[](symbol){climf}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){clim_vn}<LEND>[call](){}<LSEP>[](symbol){readDWD}<LSEP>[](symbol){file}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){clim_vnf}<LEND>[call](){}<LSEP>[](symbol){readDWD}<LSEP>[](symbol){file}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 9; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equivalent}<LEND>[](symbol){clim}<LSEP>[](symbol){clim_vn}<LEND>[statement 10; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[](symbol){clim_vn}<LSEP>[](symbol){clim_vnf}<LEND>[statement 8; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){readDWD.data works for 10 minu...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){link}<LEND>[call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){Kiel-Holtenau}<LSEP>[argument 1; litteral](str){10_minutes}<LSEP>[argument 2; litteral](str){air_temperature}<LSEP>[argument 3; litteral](str){recent}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){file}<LEND>[call](){}<LSEP>[](symbol){dataDWD}<LSEP>[](symbol){link}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[](symbol){dir_data}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){air_temperature}<LEND>[call](){}<LSEP>[](symbol){readDWD}<LSEP>[](symbol){file}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){time_diff}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){air_temperature}<LSEP>[](symbol){MESS_DATUM}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[](symbol){time_diff}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[argument 1; litteral](real){9.000000}<LEND>[statement 9; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){readDWD messages subfunctions ...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){link}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){Potsdam}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){hr}<LEND>[argument 1; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){h}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){file}<LEND>[call](){}<LSEP>[](symbol){dataDWD}<LSEP>[](symbol){link}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[](symbol){dir_data}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_message}<LEND>[argument 0; call](){}<LSEP>[](symbol){readDWD}<LSEP>[](symbol){file}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[argument 1; litteral](str){Reading 3 files with readDWD.d...}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 10; control flow](){if}<LSEP>[](symbol){radar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){++ Testing readRadarFile}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.exists}<LSEP>[](symbol){dir_exmpl}<LEND>[true branch; call](){}<LSEP>[](symbol){dir.create}<LSEP>[](symbol){dir_exmpl}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){readRadarFile works}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){trr}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){file}<LSEP>[](symbol){ext}<LSEP>[](symbol){readdwd}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){main}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){file}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){file2}<LEND>[call](){}<LSEP>[](symbol){localtestdir}<LSEP>[argument 0; litteral](str){misc}<LSEP>[](symbol){file}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rrf}<LEND>[control flow](){if}<LSEP>[](symbol){readdwd}<LEND>[true branch; call](){}<LSEP>[](symbol){readDWD}<LSEP>[](symbol){file2}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[false branch; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dwdradar}<LSEP>[](symbol){readRadarFile}<LEND>[](symbol){file2}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){rrr}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){raster}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rrf}<LSEP>[](symbol){dat}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){rrp}<LEND>[call](){}<LSEP>[](symbol){projectRasterDWD}<LSEP>[](symbol){rrr}<LSEP>[](symbol){ext}<LEND>[statement 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){plot}<LEND>[](symbol){rrr}<LSEP>[argument 1; litteral](str){\nOriginal}<LEND>[statement 6; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){plot}<LEND>[](symbol){rrp}<LSEP>[argument 1; litteral](str){\nProjected}<LEND>[statement 7; call](){}<LSEP>[](symbol){addBorders}<LEND>[statement 8; call](){}<LSEP>[](symbol){title}<LSEP>[](symbol){main}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.100000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){rngr}<LEND>[call](){}<LSEP>[](symbol){range}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){cellStats}<LEND>[](symbol){rrr}<LSEP>[argument 1; litteral](str){range}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){rngp}<LEND>[call](){}<LSEP>[](symbol){range}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){cellStats}<LEND>[](symbol){rrp}<LSEP>[argument 1; litteral](str){range}<LEND>[statement 11; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){file2}<LSEP>[](symbol){rrp}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rrf}<LSEP>[](symbol){meta}<LEND>[](symbol){rngr}<LSEP>[](symbol){rngp}<LEND>[statement 1; call](){}<LSEP>[](symbol){pdf}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){dir_exmpl}<LSEP>[argument 1; litteral](str){/Radartests.pdf}<LEND>[argument 1; litteral](real){10.000000}<LSEP>[argument 2; litteral](real){7.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){0.700000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){w1}<LEND>[call](){}<LSEP>[](symbol){trr}<LSEP>[argument 0; litteral](str){raa01-rw2017.002_10000-1712310...}<LSEP>[argument 1; litteral](str){rw}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){w2}<LEND>[call](){}<LSEP>[](symbol){trr}<LSEP>[argument 0; litteral](str){raa01-rw_10000-1907311350-dwd-...}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){rw}<LEND>[call](){}<LSEP>[](symbol){trr}<LSEP>[argument 0; litteral](str){raa01-rw_10000-1907010950-dwd-...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){sf}<LEND>[call](){}<LSEP>[](symbol){trr}<LSEP>[argument 0; litteral](str){raa01-sf_10000-1605010450-dwd-...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){rx}<LEND>[call](){}<LSEP>[](symbol){trr}<LSEP>[argument 0; litteral](str){raa01-rx_10000-1605290600-dwd-...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){rx1}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){raster}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dwdradar}<LSEP>[](symbol){readRadarFile}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rx}<LSEP>[](symbol){file}<LEND>[](symbol){dat}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){rx2}<LEND>[call](){}<LSEP>[](symbol){projectRasterDWD}<LSEP>[](symbol){rx1}<LSEP>[argument 1; litteral](NULL){NULL}<LEND>[statement 10; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){plot}<LEND>[](symbol){rx2}<LSEP>[argument 1; litteral](str){\nProjected without latlon}<LEND>[statement 11; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rx}<LSEP>[](symbol){rrp}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rx}<LSEP>[](symbol){range_orig}<LEND>[argument 2; litteral](str){\nProjected, with custom zlim}<LEND>[statement 12; call](){}<LSEP>[](symbol){addBorders}<LEND>[statement 13; call](){}<LSEP>[](symbol){dev.off}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){interactive}<LEND>[true branch; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){openFile}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){dir_exmpl}<LSEP>[argument 1; litteral](str){/Radartests.pdf}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){rangecheck}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rr}<LSEP>[](symbol){orig}<LSEP>[](symbol){proj}<LSEP>[](symbol){tolerance}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){name}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){rr}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){is}<LSEP>[](symbol){should}<LSEP>[](symbol){msg}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eq}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){almost.equal}<LEND>[](symbol){is}<LSEP>[](symbol){should}<LSEP>[](symbol){tolerance}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){eq}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[](symbol){msg}<LSEP>[argument 1; litteral](str){ not correct for: }<LSEP>[](symbol){name}<LSEP>[argument 3; litteral](str){\n}<LEND>[argument 4; call](){}<LSEP>[](symbol){toString}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){is}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 5; litteral](str){ instead of }<LEND>[argument 6; call](){}<LSEP>[](symbol){toString}<LSEP>[](symbol){should}<LEND>[argument 7; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){rc}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rr}<LSEP>[](symbol){range_orig}<LEND>[](symbol){orig}<LSEP>[argument 2; litteral](str){Range (unprojected)}<LEND>[statement 3; call](){}<LSEP>[](symbol){rc}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rr}<LSEP>[](symbol){range_proj}<LEND>[](symbol){proj}<LSEP>[argument 2; litteral](str){Range (projected)}<LEND>[statement 16; call](){}<LSEP>[](symbol){rangecheck}<LSEP>[](symbol){w1}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){6.200000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){5.870000}<LEND>[statement 17; call](){}<LSEP>[](symbol){rangecheck}<LSEP>[](symbol){w2}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){72.600000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.190000}<LEND>[argument 1; litteral](real){70.980000}<LEND>[statement 18; call](){}<LSEP>[](symbol){rangecheck}<LSEP>[](symbol){rw}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){30.700000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.450000}<LEND>[argument 1; litteral](real){30.450000}<LEND>[statement 19; call](){}<LSEP>[](symbol){rangecheck}<LSEP>[](symbol){sf}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){39.200000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.030000}<LEND>[argument 1; litteral](real){38.200000}<LEND>[statement 20; call](){}<LSEP>[](symbol){rangecheck}<LSEP>[](symbol){rx}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){31.500000}<LSEP>[argument 1; litteral](real){95.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){18.300000}<LSEP>[argument 1; litteral](real){97.170000}<LEND>[statement 11; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){++ Testing findID + selectDWD}<LEND>[statement 12; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){findID warns as wanted}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){findID}<LSEP>[argument 0; litteral](str){this_is_not_a_city}<LEND>[argument 1; litteral](str){findID: no ID could be determi...}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){findID}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Wuppertal}<LSEP>[argument 1; litteral](str){this_is_not_a_city}<LEND>[argument 1; litteral](str){findID: no ID could be determi...}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){findID}<LSEP>[argument 0; litteral](real){7777.000000}<LEND>[argument 1; litteral](str){findID: no ID could be determi...}<LEND>[statement 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){findID}<LSEP>[argument 0; litteral](str){01050}<LEND>[argument 1; litteral](str){findID: no ID could be determi...}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){findID}<LEND>[argument 1; litteral](str){}<LEND>[statement 13; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){indexFTP warns and works as in...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){base}<LSEP>[litteral](str){https://opendata.dwd.de/weathe...}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){indexFTP}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){tempdir}<LEND>[argument 3; litteral](logical){TRUE}<LEND>[argument 1; litteral](str){base should start with ftp://}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){base}<LSEP>[litteral](str){ftp://opendata.dwd.de/weather/...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){rw}<LEND>[call](){}<LSEP>[](symbol){indexFTP}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){tempdir}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){tail}<LSEP>[](symbol){rw}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){/raa01-rw_10000-latest-dwd---bin}<LEND>[statement 14; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){selectDWD works}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){link}<LEND>[call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){Potsdam}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){recent}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[](symbol){link}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){dwdbase}<LSEP>[argument 1; litteral](str){/daily/kl/recent/tageswerte_KL...}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){Potsdam}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){solar}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){dwdbase}<LSEP>[argument 1; litteral](str){/daily/solar/tageswerte_ST_039...}<LEND>[statement 15; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){selectDWD id input can be nume...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){00386}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){historical}<LEND>[argument 1; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](real){386.000000}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){historical}<LEND>[statement 16; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){selectDWD can choose Beschreib...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){00386}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){h}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){dwdbase}<LSEP>[argument 1; litteral](str){/daily/kl/historical/KL_Tagesw...}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){00386}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){h}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){daily}<LSEP>[argument 1; litteral](str){kl}<LSEP>[argument 2; litteral](str){h}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 17; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){selectDWD properly vectorizes}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_type}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){01050}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LEND>[argument 3; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){r}<LSEP>[argument 1; litteral](str){h}<LEND>[argument 1; litteral](str){list}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_type}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){01050}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){rh}<LEND>[argument 1; litteral](str){character}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){allzip_id}<LEND>[call](){}<LSEP>[](symbol){selectDWD}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1050.000000}<LSEP>[argument 1; litteral](real){386.000000}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){allzip_folder}<LEND>[call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){recent}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){allzip_id}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_gte}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){allzip_id}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){200.000000}<LEND>[statement 6; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_gte}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){allzip_id}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){7.000000}<LEND>[statement 7; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_gte}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){allzip_folder}<LEND>[argument 1; litteral](real){573.000000}<LEND>[statement 18; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){selectDWD uses remove_dupli co...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fi}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[argument 0; litteral](str){aa}<LSEP>[argument 1; litteral](str){bb}<LSEP>[argument 2; litteral](str){cc}<LSEP>[argument 3; litteral](real){42.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){as.Date}<LSEP>[argument 0; litteral](str){1989-07-01}<LEND>[argument 5; call](){}<LSEP>[](symbol){as.Date}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){2016-12-31}<LSEP>[argument 1; litteral](str){2015-12-31}<LEND>[argument 6; litteral](logical){FALSE}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){longer}<LSEP>[argument 1; litteral](str){shorter}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_length}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){aa}<LSEP>[argument 1; litteral](str){bb}<LSEP>[argument 2; litteral](str){cc}<LSEP>[argument 3; litteral](real){42.000000}<LSEP>[](symbol){fi}<LSEP>[argument 5; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_length}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){aa}<LSEP>[argument 1; litteral](str){bb}<LSEP>[argument 2; litteral](str){cc}<LSEP>[argument 3; litteral](real){42.000000}<LSEP>[](symbol){fi}<LSEP>[argument 5; litteral](logical){TRUE}<LSEP>[argument 6; litteral](logical){FALSE}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){aa}<LSEP>[argument 1; litteral](str){bb}<LSEP>[argument 2; litteral](str){cc}<LSEP>[argument 3; litteral](real){42.000000}<LSEP>[](symbol){fi}<LEND>[argument 1; litteral](str){selectDWD: duplicate file on F...}<LEND>[statement 19; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){++ Testing selectDWD warnings}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){oop}<LEND>[call](){}<LSEP>[](symbol){options}<LSEP>[argument 0; litteral](logical){FALSE}<LEND>[statement 21; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){selectDWD warns as intended}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LEND>[argument 1; litteral](str){selectDWD: neither station ID ...}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](real){7777.000000}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; litteral](str){selectDWD -> findID: no ID cou...}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](real){7777.000000}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; litteral](str){selectDWD: neither station ID ...}<LEND>[statement 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](real){7777.000000}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; litteral](str){selectDWD: in file index 'file...}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){}<LSEP>[argument 1; litteral](str){dummy}<LSEP>[argument 2; litteral](str){dummy}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; litteral](str){according to file index 'fileI...}<LEND>[statement 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){}<LSEP>[argument 1; litteral](str){dummy}<LSEP>[argument 2; litteral](str){dummy}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; litteral](str){according to file index 'fileI...}<LEND>[statement 6; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){dummy}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LEND>[argument 1; litteral](str){selectDWD: neither station ID ...}<LEND>[statement 7; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){daily}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){r}<LEND>[argument 1; litteral](str){selectDWD: neither station ID ...}<LEND>[statement 8; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){daily}<LSEP>[argument 1; litteral](str){kl}<LSEP>[argument 2; litteral](str){}<LEND>[argument 1; litteral](str){according to file index 'fileI...}<LEND>[statement 9; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){01050}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){daily}<LSEP>[argument 1; litteral](str){monthly}<LEND>[argument 2; litteral](str){kl}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; litteral](str){according to file index 'fileI...}<LEND>[statement 10; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){00386}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[argument 1; litteral](str){meta is ignored if id is given...}<LEND>[statement 11; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){Potsdam}<LSEP>[argument 1; litteral](str){multi_annual}<LSEP>[argument 2; litteral](str){mean_81-10}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; litteral](str){selectDWD: multi_annual data i...}<LEND>[statement 12; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){multi_annual}<LSEP>[argument 1; litteral](str){mean_81-10}<LSEP>[argument 2; litteral](str){r}<LEND>[argument 1; litteral](str){selectDWD: multi_annual data i...}<LEND>[statement 13; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_error}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){Potsdam}<LSEP>[argument 1; litteral](str){daily}<LSEP>[argument 2; litteral](str){solar}<LEND>[argument 1; litteral](str){selectDWD: id may not contain ...}<LEND>[statement 14; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_error}<LEND>[argument 0; call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LSEP>[argument 4; litteral](str){}<LEND>[argument 1; litteral](str){selectDWD: current=TRUE, but n...}<LEND>[statement 22; call](){}<LSEP>[](symbol){options}<LSEP>[](symbol){oop}<LEND>[statement 23; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){oop}<LEND>[statement 24; control flow](){if}<LSEP>[](symbol){index}<LEND>[true branch; call](){}<LSEP>[](symbol){checkIndex}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){metaIndex}<LSEP>[](symbol){geoIndex}<LSEP>[](symbol){indexfast}<LEND>[argument 4; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){dir_exmpl}<LSEP>[argument 1; litteral](str){/warnings.txt}<LEND>[argument 5; litteral](logical){FALSE}<LEND>[statement 25; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){++ Testing index up to date?}<LEND>[statement 26; control flow](){if}<LSEP>[](symbol){all_Potsdam_files}<LEND>[true branch; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){index is up to date - all file...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){links}<LEND>[call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){Potsdam}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){toexclude}<LEND>[call](){}<LSEP>[](symbol){grep}<LSEP>[argument 0; litteral](str){1_minute}<LSEP>[](symbol){links}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){toexclude}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){toexclude}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){toexclude}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){toexclude}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){toexclude}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){grep}<LSEP>[argument 0; litteral](str){10_minutes}<LSEP>[](symbol){links}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){files}<LEND>[call](){}<LSEP>[](symbol){dataDWD}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){links}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){toexclude}<LEND>[](symbol){dir_data}<LSEP>[argument 2; litteral](logical){NA}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](logical){FALSE}<LSEP>[argument 5; litteral](logical){FALSE}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){contents}<LEND>[call](){}<LSEP>[](symbol){readDWD}<LSEP>[](symbol){files}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 27; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){assuming updateIndexes() has b...}<LEND>[statement 28; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){test_that}<LEND>[argument 0; litteral](str){historical files have been upd...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lastyear}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.Date}<LEND>[argument 1; litteral](str){%Y}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){outdated}<LEND>[call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){end}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.Date}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){lastyear}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){-12-31}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){per}<LEND>[argument 1; litteral](str){historical}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){res}<LEND>[argument 1; litteral](str){1_minute}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){outdated}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){outdated}<LEND>[litteral](logical){FALSE}<LEND>[statement 3; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){outdated}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){outdated}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rvp}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){outdated}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){alloutdated}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){rvp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fi}<LEND>[call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rvp}<LSEP>[](symbol){r}<LSEP>[argument 2; litteral](str){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){var}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rvp}<LSEP>[](symbol){r}<LSEP>[argument 2; litteral](str){var}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){per}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rvp}<LSEP>[](symbol){r}<LSEP>[argument 2; litteral](str){per}<LEND>[statement 1; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fi}<LSEP>[](symbol){outdated}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rvp}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){rvp}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){paste}<LSEP>[argument 3; litteral](str){/}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){rvp}<LEND>[call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){rvp}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){alloutdated}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The DWD has not yet updated an...}<LSEP>[argument 1; litteral](str){the following }<LEND>[argument 2; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){alloutdated}<LEND>[argument 3; litteral](str){ folders:\n}<LEND>[argument 4; call](){}<LSEP>[](symbol){toString}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rvp}<LSEP>[](symbol){alloutdated}<LEND>[statement 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){testthat}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 29; control flow](){if}<LSEP>[](symbol){devcheck}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){checkSuggestedPackage}<LSEP>[argument 0; litteral](str){devtools}<LSEP>[argument 1; litteral](str){runLocalTests with devcheck=TRUE}<LEND>[statement 1; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){++ Running devtools::check. Th...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){devtools}<LSEP>[](symbol){check}<LEND>[](symbol){quiet}<LEND>[statement 3; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){dd}<LEND>[statement 30; control flow](){if}<LSEP>[](symbol){examples}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){checkSuggestedPackage}<LSEP>[argument 0; litteral](str){roxygen2}<LSEP>[argument 1; litteral](str){runLocalTests with examples=TRUE}<LEND>[statement 1; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){++ Testing examples}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){devcheck}<LEND>[true branch; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){roxygen2}<LSEP>[](symbol){roxygenise}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){oo}<LEND>[call](){}<LSEP>[](symbol){options}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){testExamples}<LEND>[](symbol){dir_exmpl}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 5; call](){}<LSEP>[](symbol){options}<LSEP>[](symbol){oo}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){logfile}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){dir_exmpl}<LSEP>[argument 1; litteral](str){/warnings.txt}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){log}<LEND>[call](){}<LSEP>[](symbol){readLines}<LSEP>[](symbol){logfile}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){log}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){log}<LSEP>[argument 1; litteral](str){\n}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){rem}<LSEP>[litteral](str){\nList of 8\n \\$ Metadaten_Fe...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){log}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[](symbol){rem}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){log}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){rem}<LSEP>[litteral](str){Warning: fileType failed for t...}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){log}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[](symbol){rem}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){log}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){rem}<LSEP>[litteral](str){\nrdwd station id 2849 with 3 ...}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){log}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[](symbol){rem}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){log}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){rem}<LSEP>[litteral](str){\nNote in is.error: Error in p...}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){log}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[](symbol){rem}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){log}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){rem}<LSEP>[litteral](str){\nFormal class 'RasterBrick' [...}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){log}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[](symbol){rem}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){log}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){rem}<LSEP>[litteral](str){---------------\nC:/Dropbox/Rp...}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){log}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){rem}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){log}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){rem}<LSEP>[litteral](str){---------------\nC:/Dropbox/Rp...}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){log}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[](symbol){rem}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){log}<LEND>[statement 23; call](){}<LSEP>[](symbol){cat}<LSEP>[](symbol){log}<LSEP>[](symbol){logfile}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){runtime}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){difftime}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[](symbol){begintime}<LSEP>[argument 2; litteral](str){min}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 32; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){++ Testing finished! Total ru...}<LSEP>[](symbol){runtime}<LSEP>[argument 2; litteral](str){ minutes}<LEND>[statement 33; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){runtime}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.report.monomorphs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){hold}<LSEP>[](symbol){x}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){na.counter}<LSEP>[litteral](real){0.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){loc.list}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Identifying monomorphic loci\n}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SilicoDArT}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lN}<LEND>[call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){x}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){row}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){row}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){row}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){row}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loc.list}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lN}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){row}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){na.counter}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){na.counter}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SNP}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lN}<LEND>[call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){x}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){row}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){row}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){row}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){row}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loc.list}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lN}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){row}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){na.counter}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){na.counter}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){loc.list}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loc.list}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){loc.list}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){loc.list}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.drop.loc}<LSEP>[](symbol){x}<LSEP>[](symbol){loc.list}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 15; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n No. of loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){hold}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 16; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Polymorphic loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 17; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Monomorphic loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){hold}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[](symbol){na.counter}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 18; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Loci scored all NA:}<LSEP>[](symbol){na.counter}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 19; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of individuals:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 20; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of populations:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n\n}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 22; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.pcoa.scree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){top}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){s}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){eig}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){e}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){eig}<LEND>[argument 1; litteral](real){100.000000}<LEND>[](symbol){s}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){top}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){e}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){e}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){e}<LEND>[argument 1; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){e}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Note: Only eigenvalues for d...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Note: All eigenvalues shown\n}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){top}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){e}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){e}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of axes each explaining ...}<LSEP>[](symbol){top}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){e}<LEND>[](symbol){e}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){m}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){eigenvalue}<LSEP>[argument 1; litteral](str){percent}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){xlab}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Eigenvalue}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){ylab}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Percentage Contribution}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ggplot}<LSEP>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){eigenvalue}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){percent}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_point}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](str){red}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_line}<LSEP>[argument 0; litteral](str){red}<LEND>[argument 1; call](){}<LSEP>[](symbol){ggtitle}<LSEP>[argument 0; litteral](str){Scree plot for PCoA}<LEND>[argument 1; call](){}<LSEP>[](symbol){theme}<LEND>[argument 0; call](){}<LSEP>[](symbol){element_text}<LSEP>[argument 0; litteral](str){bold.italic}<LSEP>[argument 1; litteral](str){20}<LSEP>[argument 2; litteral](str){black}<LEND>[argument 1; call](){}<LSEP>[](symbol){element_text}<LSEP>[argument 0; litteral](str){bold}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){16.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){element_text}<LSEP>[argument 0; litteral](str){bold}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){16.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){labs}<LSEP>[](symbol){xlab}<LSEP>[](symbol){ylab}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_hline}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_vline}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){top}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_hline}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){e}<LEND>[argument 1; litteral](str){blue}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 18; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){p}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){is.foldermtg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){foldermtg}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}

[](){expression}<LSEP>[litteral](str){metadata_withreplic_example}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matddjeffreyspar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){freq}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){freq}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){freq}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){freq}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){freq}<LEND>[body; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){ddjeffreyspar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){freq}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){freq}<LSEP>[](symbol){j}<LEND>[statement 3; call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){distances}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rmrow.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){name}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){object}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){rmrow.folder applies to an obj...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){objk}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){object}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xf}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){objk}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){objk}<LEND>[](symbol){name}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){object}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){xf}

[](){expression}<LSEP>[litteral](str){metadata_large_example}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){summary.foldert}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){summ.fold}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){object}<LSEP>[](symbol){summary}<LSEP>[](symbol){...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){summ.fold}<LSEP>[argument 1; litteral](str){times}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){times}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){summ.fold}<LSEP>[argument 1; litteral](str){same.rows}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){same.rows}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){summ.fold}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rt_ticket_history_reply}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){ticket_id}<LSEP>[](symbol){text}<LSEP>[](symbol){cc}<LSEP>[](symbol){bcc}<LSEP>[](symbol){time_worked}<LSEP>[](symbol){attachment_path}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){params}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){ticket_id}<LSEP>[argument 1; litteral](str){correspond}<LSEP>[](symbol){text}<LSEP>[](symbol){cc}<LSEP>[](symbol){bcc}<LSEP>[](symbol){time_worked}<LSEP>[](symbol){attachment_path}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){url}<LEND>[call](){}<LSEP>[](symbol){rt_url}<LSEP>[argument 0; litteral](str){ticket}<LSEP>[](symbol){ticket_id}<LSEP>[argument 2; litteral](str){comment}<LSEP>[](symbol){params}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){reply_body}<LEND>[call](){}<LSEP>[](symbol){construct_newline_pairs}<LSEP>[](symbol){params}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){response}<LEND>[call](){}<LSEP>[](symbol){rt_POST}<LSEP>[](symbol){url}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){reply_body}<LEND>[](symbol){...}<LEND>[statement 4; call](){}<LSEP>[](symbol){stopforstatus}<LSEP>[](symbol){response}<LEND>[statement 5; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){ticket_id}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.plot}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){labels}<LSEP>[](symbol){indlabels}<LSEP>[](symbol){col}<LSEP>[](symbol){legend}<LSEP>[](symbol){posi}<LSEP>[](symbol){bg}<LSEP>[](symbol){verbose}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Fatal Error: genlight object...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Population assignments not d...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](str){pop1}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){gl.filter.monomorphs}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){tmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: genlight object con...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){labels}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){adegenet}<LSEP>[](symbol){glPlot}<LEND>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){X}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){X}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){X}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){X}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){indlabels}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){indlabes}<LEND>[call](){}<LSEP>[](symbol){pretty}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){5.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){col}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){myCol}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){colorRampPalette}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){royalblue3}<LSEP>[argument 1; litteral](str){firebrick1}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){X}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){myCol}<LSEP>[](symbol){col}<LEND>[statement 4; call](){}<LSEP>[](symbol){image}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[](symbol){X}<LSEP>[argument 3; litteral](str){SNP index}<LSEP>[argument 4; litteral](str){n}<LSEP>[](symbol){myCol}<LSEP>[argument 6; litteral](str){}<LSEP>[](symbol){...}<LEND>[statement 5; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){indlabels}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){legend}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){legend}<LSEP>[](symbol){posi}<LSEP>[](symbol){myCol}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){X}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 3; litteral](logical){TRUE}<LSEP>[](symbol){bg}<LSEP>[argument 5; litteral](str){Number of 2nd allele}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 11; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){logistic}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){rrreg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){formula}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){data}<LSEP>[](symbol){start}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){matrixMethod}<LSEP>[](symbol){maxIter}<LSEP>[](symbol){verbose}<LSEP>[](symbol){optim}<LSEP>[](symbol){em.converge}<LSEP>[](symbol){glmMaxIter}<LSEP>[](symbol){solve.tolerance}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){model.frame}<LSEP>[](symbol){formula}<LSEP>[](symbol){data}<LSEP>[](symbol){na.omit}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){model.matrix.default}<LSEP>[](symbol){formula}<LSEP>[](symbol){df}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){bscale}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){unname}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sd}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){sweep}<LSEP>[](symbol){x1}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){bscale}<LSEP>[](symbol){/}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){model.response}<LSEP>[](symbol){df}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){cd}<LEND>[call](){}<LSEP>[](symbol){rrcd}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){cd}<LSEP>[](symbol){c}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){cd}<LSEP>[](symbol){d}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){design}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Missing design specification, ...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){forced-known}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){mirrored}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){disguised}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){unrelated-known}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){The design you specified,}<LSEP>[](symbol){design}<LSEP>[argument 2; litteral](str){is not implemented in this ver...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){obs.llik}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){par}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){gx}<LSEP>[](symbol){bayesglm}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){gx}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){gx}<LEND>[call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){par}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){llik}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){gx}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){gx}<LEND>[](symbol){d}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){llik}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){h}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){group}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Need to specify character vect...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){h}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){group}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Need to specify named vector o...}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){aux.check}<LEND>[call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){h}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){group}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){start}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){start}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The starting values are not th...}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){start}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){par}<LSEP>[](symbol){start}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){par}<LEND>[call](){}<LSEP>[](symbol){rnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){gx}<LEND>[call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){par}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){pllik}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){inf}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){llik}<LEND>[call](){}<LSEP>[](symbol){obs.llik}<LSEP>[](symbol){par}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){gx}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){counter}<LSEP>[litteral](real){0.000000}<LEND>[statement 19; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){llik}<LSEP>[](symbol){pllik}<LEND>[](symbol){em.converge}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){counter}<LSEP>[](symbol){maxIter}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){w1}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){gx}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){gx}<LEND>[](symbol){d}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){w0}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){gx}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){gx}<LEND>[](symbol){d}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){n}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w0}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w1}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){lfit}<LEND>[call](){}<LSEP>[](symbol){glm}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){binomial}<LSEP>[argument 0; litteral](str){logit}<LEND>[](symbol){w}<LSEP>[](symbol){par}<LEND>[argument 4; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){glmMaxIter}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){par}<LEND>[call](){}<LSEP>[](symbol){coef}<LSEP>[](symbol){lfit}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){gx}<LEND>[call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){par}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){pllik}<LSEP>[](symbol){llik}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[](symbol){T}<LEND>[true branch; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){counter}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){llik}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){llik}<LEND>[call](){}<LSEP>[](symbol){obs.llik}<LSEP>[](symbol){par}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){gx}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){counter}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){counter}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){llik}<LSEP>[](symbol){pllik}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){log-likelihood is not monotoni...}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){counter}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){maxIter}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){number of iterations exceeded ...}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){bpar}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){par}<LSEP>[](symbol){bscale}<LEND>[statement 21; control flow](){if}<LSEP>[](symbol){optim}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){MLEfit}<LEND>[call](){}<LSEP>[](symbol){optim}<LSEP>[](symbol){par}<LSEP>[](symbol){obs.llik}<LSEP>[argument 2; litteral](str){BFGS}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[argument 5; litteral](logical){TRUE}<LEND>[argument 6; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){c}<LSEP>[](symbol){d}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){MLEfit}<LSEP>[](symbol){hessian}<LEND>[](symbol){solve.tolerance}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){vcov}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){bscale}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){bscale}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){vcov}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){score.rr}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){gx}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){c}<LEND>[](symbol){gx}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){gx}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){gx}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){c}<LEND>[](symbol){gx}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){gx}<LEND>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){information.rr}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){crossprod}<LSEP>[](symbol){score.rr}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){information.rr}<LSEP>[](symbol){solve.tolerance}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){vcov}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){bscale}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){bscale}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){vcov}<LEND>[statement 22; control flow](){if}<LSEP>[](symbol){aux.check}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dlogistic.coef}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){score}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){w}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){coef}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){dlogistic.coef}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){w.coef}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){coef}<LEND>[](symbol){w}<LEND>[statement 4; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colSums}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w.coef}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){jbn}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){w}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){coef1}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){y}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){coef2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){c}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[](symbol){d}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){c}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[](symbol){d}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){coef1}<LSEP>[](symbol){coef2}<LEND>[](symbol){x}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){gmm}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){W}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){w}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){score}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){group.labels}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){h}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){h}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wg}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){g}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){h}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){W}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){m1}<LSEP>[](symbol){g}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){m1}<LSEP>[](symbol){g}<LEND>[](symbol){W}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){m1}<LSEP>[](symbol){g}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){grad}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){W}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){w}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){score}<LEND>[call](){}<LSEP>[](symbol){score}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){jbn}<LEND>[call](){}<LSEP>[](symbol){jbn}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){group.labels}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){h}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){h}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wg}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){g}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){h}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){grad.iter}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colSums}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){dlogistic.coef}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){jbn}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){jbn}<LSEP>[](symbol){grad.iter}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){W}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){score}<LSEP>[](symbol){g}<LEND>[statement 8; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){score}<LSEP>[](symbol){g}<LEND>[](symbol){W}<LEND>[](symbol){jbn}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){weight.matrix}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){matrixMethod}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){w}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){coef}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){dlogistic.coef}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){beta}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){w.coef}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){coef}<LEND>[](symbol){w}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){dg}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){group.labels}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){h}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){group.labels}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wg}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dg}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){h}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[](symbol){beta}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){matrix1}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w.coef}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w.coef}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){matrix2}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){dg}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dg}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){efficient.W}<LEND>[call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){adiag}<LSEP>[](symbol){matrix1}<LSEP>[](symbol){matrix2}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){matrixMethod}<LSEP>[argument 1; litteral](str){efficient}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){matrixMethod}<LSEP>[argument 1; litteral](str){cue}<LEND>[true branch; block](){}<LSEP>[](symbol){efficient.W}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){matrixMethod}<LSEP>[argument 1; litteral](str){princomp}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){decomp}<LEND>[call](){}<LSEP>[](symbol){eigen}<LSEP>[](symbol){efficient.W}<LEND>[statement 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){decomp}<LSEP>[](symbol){values}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){decomp}<LSEP>[](symbol){vectors}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){decomp}<LSEP>[](symbol){vectors}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){gmm.cue}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){matrixMethod}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){w}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){m1}<LEND>[call](){}<LSEP>[](symbol){score}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){group.labels}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){h}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){h}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wg}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){g}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){h}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){weight.matrix}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){matrixMethod}<LEND>[statement 7; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){m1}<LSEP>[](symbol){g}<LEND>[](symbol){W}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){m1}<LSEP>[](symbol){g}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){rr.true.coefs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){W}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){matrixMethod}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){w}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){W}<LEND>[argument 1; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){h}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){W}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[](symbol){h}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){matrixMethod}<LSEP>[argument 1; litteral](str){efficient}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){matrixMethod}<LSEP>[argument 1; litteral](str){princomp}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){weight.matrix}<LEND>[call](){}<LSEP>[](symbol){weight.matrix}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){matrixMethod}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){fit1}<LEND>[call](){}<LSEP>[](symbol){optim}<LSEP>[](symbol){beta}<LSEP>[](symbol){gmm}<LSEP>[](symbol){grad}<LSEP>[argument 3; litteral](str){BFGS}<LEND>[argument 4; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](real){500.000000}<LEND>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){weight.matrix}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){newpar}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fit1}<LSEP>[](symbol){par}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){weight.matrix}<LEND>[call](){}<LSEP>[](symbol){weight.matrix}<LSEP>[](symbol){newpar}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){matrixMethod}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){fit2}<LEND>[call](){}<LSEP>[](symbol){optim}<LSEP>[](symbol){newpar}<LSEP>[](symbol){gmm}<LSEP>[](symbol){grad}<LSEP>[argument 3; litteral](str){BFGS}<LEND>[argument 4; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](real){500.000000}<LEND>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){weight.matrix}<LEND>[](symbol){fit2}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fit}<LEND>[call](){}<LSEP>[](symbol){optim}<LSEP>[](symbol){beta}<LSEP>[](symbol){gmm.cue}<LSEP>[argument 2; litteral](str){BFGS}<LEND>[argument 3; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](real){500.000000}<LEND>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){matrixMethod}<LEND>[](symbol){fit}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){rr.true.vcov}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){matrixMethod}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){w}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){jbn}<LEND>[call](){}<LSEP>[](symbol){jbn}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){w}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){group.labels}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){h}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){group.labels}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wg}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){grad.iter}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){dlogistic.coef}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){group.labels}<LSEP>[](symbol){i}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){jbn}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){jbn}<LSEP>[](symbol){grad.iter}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){weight.matrix}<LEND>[call](){}<LSEP>[](symbol){weight.matrix}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){matrixMethod}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){matrixMethod}<LSEP>[argument 1; litteral](str){princomp}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){jbn}<LEND>[](symbol){weight.matrix}<LEND>[](symbol){jbn}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){V}<LEND>[call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){weight.matrix}<LSEP>[](symbol){beta}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[argument 7; litteral](str){efficient}<LEND>[statement 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){jbn}<LEND>[](symbol){weight.matrix}<LEND>[](symbol){jbn}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){jbn}<LEND>[](symbol){weight.matrix}<LEND>[](symbol){V}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){weight.matrix}<LEND>[](symbol){jbn}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){jbn}<LEND>[](symbol){weight.matrix}<LEND>[](symbol){jbn}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){true.fit}<LEND>[call](){}<LSEP>[](symbol){rr.true.coefs}<LSEP>[](symbol){bpar}<LSEP>[](symbol){y}<LSEP>[](symbol){x1}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){matrixMethod}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){bpar}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){true.fit}<LSEP>[](symbol){par}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){rr.true.vcov}<LSEP>[](symbol){bpar}<LSEP>[](symbol){y}<LSEP>[](symbol){x1}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LSEP>[](symbol){h}<LSEP>[](symbol){group}<LSEP>[](symbol){matrixMethod}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){vcov}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){J.stat}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){true.fit}<LSEP>[](symbol){val}<LEND>[](symbol){n}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){overid.p}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){pchisq}<LSEP>[](symbol){J.stat}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){h}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){return.object}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){bpar}<LSEP>[](symbol){vcov}<LSEP>[](symbol){se}<LSEP>[](symbol){df}<LEND>[argument 4; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[](symbol){x1}<LSEP>[](symbol){y}<LSEP>[](symbol){design}<LEND>[argument 8; call](){}<LSEP>[](symbol){match.call}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){forced-known}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){p}<LEND>[](symbol){p}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){p1}<LEND>[](symbol){p1}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){p0}<LEND>[](symbol){p0}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){mirrored}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){disguised}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){p}<LEND>[](symbol){p}<LEND>[statement 26; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){unrelated-known}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){p}<LEND>[](symbol){p}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){q}<LEND>[](symbol){q}<LEND>[statement 27; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){aux}<LEND>[](symbol){aux.check}<LEND>[statement 28; control flow](){if}<LSEP>[](symbol){aux.check}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){h}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){wm}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){matrixMethod}<LSEP>[argument 1; litteral](str){cue}<LEND>[argument 1; litteral](str){continuously updating}<LEND>[argument 2; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){matrixMethod}<LSEP>[argument 1; litteral](str){princomp}<LEND>[argument 1; litteral](str){principal components}<LSEP>[argument 2; litteral](str){efficient}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){J.stat}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){J.stat}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){overid.p}<LEND>[](symbol){overid.p}<LEND>[statement 29; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){return.object}<LEND>[litteral](str){rrreg}<LEND>[statement 30; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){return.object}<LEND>[assign](){<-}<LSEP>[](symbol){summarize.design}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){design}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){design.short}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){-}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design.short}<LSEP>[argument 1; litteral](str){forced}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){param}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){p = }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){, p0 = }<LEND>[argument 3; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){p0}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 4; litteral](str){, and p1 = }<LEND>[argument 5; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){p1}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 6; litteral](str){}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Randomized response }<LSEP>[](symbol){design.short}<LSEP>[argument 2; litteral](str){ design with }<LSEP>[](symbol){param}<LSEP>[argument 4; litteral](str){.}<LSEP>[argument 5; litteral](str){}<LEND>[assign](){<-}<LSEP>[](symbol){rrcd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){design}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Missing design specification, ...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){forced-known}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){mirrored}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){disguised}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){unrelated-known}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){The design you specified,}<LSEP>[](symbol){design}<LSEP>[argument 2; litteral](str){is not implemented in this ver...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){forced-known}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p1}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){for the forced design with kno...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){for the forced design with kno...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p1}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){for the forced design with kno...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p must be a probability}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){p1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p1 must be a probability}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p0}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){p0}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p0 must be a probability}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LEND>[](symbol){p1}<LEND>[argument 1; litteral](real){10.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p, p0, and p1 must sum to 1}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){c}<LSEP>[](symbol){p}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){d}<LSEP>[](symbol){p1}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){mirrored}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){disguised}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){for the}<LSEP>[](symbol){design}<LSEP>[argument 2; litteral](str){design, you must specify p}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p must be a probability that i...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){unrelated-known}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){q, the probability of answerin...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){q}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){for the}<LSEP>[](symbol){design}<LSEP>[argument 2; litteral](str){design, you must specify p}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){for the}<LSEP>[](symbol){design}<LSEP>[argument 2; litteral](str){design, you must specify q}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){q}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){for the}<LSEP>[](symbol){design}<LSEP>[argument 2; litteral](str){design, you must specify p and q}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p must be a probability}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){q must be a probability}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){c}<LSEP>[](symbol){p}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){q}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){c}<LSEP>[](symbol){d}<LEND>[assign](){<-}<LSEP>[](symbol){vcov.rrreg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){vcov}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){vcov}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coef.names}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){vcov}<LEND>[assign](){<-}<LSEP>[](symbol){coef.rrreg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){coef}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){coef}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coef.names}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){coef}<LEND>[assign](){<-}<LSEP>[](symbol){predict.rrreg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){given.y}<LSEP>[](symbol){alpha}<LSEP>[](symbol){n.sims}<LSEP>[](symbol){avg}<LSEP>[](symbol){newdata}<LSEP>[](symbol){quasi.bayes}<LSEP>[](symbol){keep.draws}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){z.post}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){coef}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){coef}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){coef}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){design}<LEND>[argument 1; litteral](str){forced-known}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p1}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p0}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p1}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p0}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){design}<LEND>[argument 1; litteral](str){disguised}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){design}<LEND>[argument 1; litteral](str){mirrored}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){design}<LEND>[argument 1; litteral](str){unrelated-known}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){q}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){x}<LSEP>[](symbol){coef}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){q}<LEND>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){y}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){pred}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){newdata}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xvar}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){newdata}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No data in the provided data f...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xvar}<LEND>[call](){}<LSEP>[](symbol){model.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.formula}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){~}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[](symbol){formula}<LEND>[argument 1; litteral](real){3.000000}<LEND>[](symbol){newdata}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){given.y}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){newdata1}<LEND>[call](){}<LSEP>[](symbol){model.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[](symbol){formula}<LEND>[](symbol){newdata}<LSEP>[](symbol){na.omit}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xvar}<LEND>[call](){}<LSEP>[](symbol){model.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.formula}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){~}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){call}<LEND>[](symbol){formula}<LEND>[argument 1; litteral](real){3.000000}<LEND>[](symbol){newdata1}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){model.response}<LSEP>[](symbol){newdata1}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){quasi.bayes}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){given.y}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){z.post}<LSEP>[](symbol){object}<LSEP>[](symbol){xvar}<LSEP>[](symbol){y}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xvar}<LEND>[argument 1; call](){}<LSEP>[](symbol){coef}<LSEP>[](symbol){object}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){avg}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){mean}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){return.object}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){pred}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){draws}<LEND>[call](){}<LSEP>[](symbol){mvrnorm}<LSEP>[](symbol){n.sims}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){est}<LEND>[argument 2; call](){}<LSEP>[](symbol){vcov}<LSEP>[](symbol){object}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){given.y}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){z.post}<LSEP>[](symbol){object}<LSEP>[](symbol){xvar}<LSEP>[](symbol){y}<LEND>[argument 3; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){draws}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){logistic}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){xvar}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){draws}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){avg}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){mean}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){est}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){mean}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){lower.ci}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){a}<LEND>[body; call](){}<LSEP>[](symbol){quantile}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){upper.ci}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){a}<LEND>[body; call](){}<LSEP>[](symbol){quantile}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pred}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){sd}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){return.object}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){est}<LSEP>[](symbol){se}<LSEP>[](symbol){lower.ci}<LSEP>[](symbol){upper.ci}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){keep.draws}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){return.object}<LSEP>[](symbol){qoi.draws}<LEND>[](symbol){pred}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){return.object}<LEND>[assign](){<-}<LSEP>[](symbol){summary.rrreg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){structure}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){summary.rrreg}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){print.rrreg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nRandomized Response Techniqu...}<LEND>[statement 1; call](){}<LSEP>[](symbol){dput}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){call}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){est}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){est}<LSEP>[argument 1; litteral](str){se}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){x}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){est}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){se}<LEND>[statement 8; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){tb}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 10; call](){}<LSEP>[](symbol){summarize.design}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){design}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p0}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p1}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){q}<LEND>[statement 11; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){aux}<LEND>[true branch; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Incorporating }<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){nh}<LEND>[argument 2; litteral](str){ auxiliary moment(s). Weightin...}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){wm}<LEND>[argument 4; litteral](str){.\n}<LSEP>[argument 5; litteral](str){The overidentification test st...}<LEND>[argument 6; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){J.stat}<LEND>[argument 7; litteral](str){ (p < }<LEND>[argument 8; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){overid.p}<LEND>[argument 9; litteral](str){)}<LSEP>[argument 10; litteral](str){.\n}<LSEP>[argument 11; litteral](str){}<LEND>[statement 13; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){print.summary.rrreg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nRandomized Response Techniqu...}<LEND>[statement 1; call](){}<LSEP>[](symbol){dput}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){call}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){est}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Est.}<LSEP>[argument 1; litteral](str){S.E.}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tb}<LEND>[call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){x}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){est}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tb}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){se}<LEND>[statement 8; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){tb}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 10; call](){}<LSEP>[](symbol){summarize.design}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){design}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p0}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){p1}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){q}<LEND>[statement 11; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){aux}<LEND>[true branch; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Incorporating }<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){nh}<LEND>[argument 2; litteral](str){ auxiliary moment(s). Weightin...}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){wm}<LEND>[argument 4; litteral](str){.\n}<LSEP>[argument 5; litteral](str){The overidentification test st...}<LEND>[argument 6; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){J.stat}<LEND>[argument 7; litteral](str){ (p < }<LEND>[argument 8; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){overid.p}<LEND>[argument 9; litteral](str){)}<LSEP>[argument 10; litteral](str){.\n}<LSEP>[argument 11; litteral](str){}<LEND>[statement 13; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){power.rr.test}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){n}<LSEP>[](symbol){r}<LSEP>[](symbol){presp}<LSEP>[](symbol){presp.null}<LSEP>[](symbol){sig.level}<LSEP>[](symbol){prespT}<LSEP>[](symbol){prespC}<LSEP>[](symbol){prespT.null}<LSEP>[](symbol){prespC.null}<LSEP>[](symbol){power}<LSEP>[](symbol){type}<LSEP>[](symbol){alternative}<LSEP>[](symbol){solve.tolerance}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){se.f.rr}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){n}<LSEP>[](symbol){r}<LSEP>[](symbol){presp}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){presp}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Missing probability of latent ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){n}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Missing sample size, see docum...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){forced-unknown}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){unrelated-unknown}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cd}<LEND>[call](){}<LSEP>[](symbol){rrcd}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){cd}<LSEP>[](symbol){c}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){cd}<LSEP>[](symbol){d}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){r}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){r must be a probability}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){forced-known}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){unrelated-known}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){information.rr}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){c}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){presp}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){presp}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){information.rr}<LSEP>[](symbol){solve.tolerance}<LEND>[](symbol){n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){vcov}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){mirrored}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){disguised}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){information.rr}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){c}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){presp}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){d}<LEND>[](symbol){presp}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){c}<LSEP>[](symbol){presp}<LEND>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){d}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){presp}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){d}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){information.rr}<LSEP>[](symbol){solve.tolerance}<LEND>[](symbol){n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){vcov}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){unrelated-unknown}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){q}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){for the}<LSEP>[](symbol){design}<LSEP>[argument 2; litteral](str){design, you must specify p}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){for the}<LSEP>[](symbol){design}<LSEP>[argument 2; litteral](str){design, you must specify q}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){q}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){for the}<LSEP>[](symbol){design}<LSEP>[argument 2; litteral](str){design, you must specify p and q}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p must be a probability}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){q must be a probability}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){information.rr}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){presp}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){presp}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){presp}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){presp}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){information.rr}<LSEP>[](symbol){solve.tolerance}<LEND>[](symbol){n}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){vcov}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){forced-unknown}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p1}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){for the forced design, you mus...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){for the forced design, you mus...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p1}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){for the forced design, you mus...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p must be a probability}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){p1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p1 must be a probability}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p0}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p0}<LSEP>[litteral](real){0.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p0}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){p0}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p0 must be a probability}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LEND>[](symbol){p1}<LEND>[argument 1; litteral](real){10.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p, p0, and p1 must sum to 1}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){q}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){q}<LSEP>[litteral](real){1.000000}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){q must be a probability}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){information.rr}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){presp}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){presp}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){presp}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){presp}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){information.rr}<LSEP>[](symbol){solve.tolerance}<LEND>[](symbol){n}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){vcov}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){return.object}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){vcov}<LSEP>[](symbol){se}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){return.object}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){sig.level}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Missing significance level (Ty...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){type}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Missing specification, one.sam...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){alternative}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Missing specification, one.sid...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){power}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){power}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Exactly one of 'n' or 'power' ...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){power}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){power}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Exactly one of 'n' or 'power' ...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){sig.level}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){sig.level}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Significance level must be a p...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){power}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){power}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Power must be a probability}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){forced-unknown}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){unrelated-unknown}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){r}<LSEP>[litteral](NULL){NULL}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){r}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){r must be a probability}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){power}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){one.sample}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){presp.null}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){presp.null}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){presp}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){presp}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Proportion of respondents with...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){presp.null}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){presp.null}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Null proportion of respondents...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){se.rr.alt}<LEND>[call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){n}<LSEP>[](symbol){r}<LSEP>[](symbol){presp}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){se.rr.alt}<LSEP>[](symbol){se}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){se.rr.null}<LEND>[call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){n}<LSEP>[](symbol){r}<LSEP>[](symbol){presp.null}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){se.null}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){se.rr.null}<LSEP>[](symbol){se}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){alternative}<LSEP>[argument 1; litteral](str){one.sided}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){thld.null}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){sig.level}<LEND>[](symbol){se.null}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){power}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.null}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){alternative}<LSEP>[argument 1; litteral](str){two.sided}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){thld.low}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sig.level}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){se.null}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){thld.high}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sig.level}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){se.null}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){power.low}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.low}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){power.high}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.high}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){power}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){power.low}<LSEP>[](symbol){power.high}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){two.sample}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){prespT.null}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){prespT.null}<LSEP>[](symbol){prespC.null}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){prespT}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){prespT}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){prespC}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){prespC}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Proportion of respondents with...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){prespT.null}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){prespT.null}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){prespC.null}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){prespC.null}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Null proportion of respondents...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){presp}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){prespT}<LSEP>[](symbol){prespC}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){se.rr.alt.T}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){n}<LSEP>[](symbol){r}<LSEP>[](symbol){prespT}<LEND>[](symbol){se}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){se.rr.alt.C}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){n}<LSEP>[](symbol){r}<LSEP>[](symbol){prespC}<LEND>[](symbol){se}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.alt.T}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.alt.C}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){presp.null}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){prespT.null}<LSEP>[](symbol){prespC.null}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){se.rr.null.T}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){n}<LSEP>[](symbol){r}<LSEP>[](symbol){prespT.null}<LEND>[](symbol){se}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){se.rr.null.C}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){n}<LSEP>[](symbol){r}<LSEP>[](symbol){prespC.null}<LEND>[](symbol){se}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){se.null}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.null.T}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.null.C}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){alternative}<LSEP>[argument 1; litteral](str){one.sided}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){thld.null}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){sig.level}<LEND>[](symbol){se.null}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){power}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.null}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){alternative}<LSEP>[argument 1; litteral](str){two.sided}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){thld.low}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sig.level}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){se.null}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){thld.high}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sig.level}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){se.null}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){power.low}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.low}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){power.high}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.high}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){power}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){power.low}<LSEP>[](symbol){power.high}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){n}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){forced-unknown}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){design}<LSEP>[argument 1; litteral](str){unrelated-unknown}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){N}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){100000.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){N}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){100000.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){one.sample}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){presp.null}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){presp.null}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){presp}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){presp}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Proportion of respondents with...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){presp.null}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){presp.null}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Null proportion of respondents...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){alternative}<LSEP>[argument 1; litteral](str){one.sided}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){N}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sample}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){N}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){se.rr.alt}<LEND>[call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){presp}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){se.rr.alt}<LSEP>[](symbol){se}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){se.rr.null}<LEND>[call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){presp.null}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){se.null}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){se.rr.null}<LSEP>[](symbol){se}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){thld.null}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){sig.level}<LEND>[](symbol){se.null}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){power.n}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.null}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){power}<LSEP>[](symbol){power.n}<LEND>[argument 1; litteral](real){0.010000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){N}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){break}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){sample}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){N}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Your n exceeds 100,000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){alternative}<LSEP>[argument 1; litteral](str){two.sided}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){N}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sample}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){N}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){se.rr.alt}<LEND>[call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){presp}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){se.rr.alt}<LSEP>[](symbol){se}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){se.rr.null}<LEND>[call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){presp.null}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){se.null}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){se.rr.null}<LSEP>[](symbol){se}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){thld.low}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sig.level}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){se.null}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){thld.high}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sig.level}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){se.null}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){power.low}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.low}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){power.high}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.high}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){power.n}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){power.low}<LSEP>[](symbol){power.high}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){power}<LSEP>[](symbol){power.n}<LEND>[argument 1; litteral](real){0.010000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){N}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){break}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){sample}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){N}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Your n exceeds 100,000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){two.sample}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){prespT.null}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){prespT.null}<LSEP>[](symbol){prespC.null}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){prespT}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){prespT}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){prespC}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){prespC}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Proportion of respondents with...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){prespT.null}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){prespT.null}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){prespC.null}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){prespC.null}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Null proportion of respondents...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){alternative}<LSEP>[argument 1; litteral](str){one.sided}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){N}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sample}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){N}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){presp}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){prespT}<LSEP>[](symbol){prespC}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){se.rr.alt.T}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){prespT}<LEND>[](symbol){se}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){se.rr.alt.C}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){prespC}<LEND>[](symbol){se}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.alt.T}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.alt.C}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){presp.null}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){prespT.null}<LSEP>[](symbol){prespC.null}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){se.rr.null.T}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){prespT.null}<LEND>[](symbol){se}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){se.rr.null.C}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){prespC.null}<LEND>[](symbol){se}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){se.null}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.null.T}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.null.C}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){thld.null}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){sig.level}<LEND>[](symbol){se.null}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){power.n}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.null}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){power}<LSEP>[](symbol){power.n}<LEND>[argument 1; litteral](real){0.010000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){N}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){break}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){sample}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){N}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Your n exceeds 100,000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){alternative}<LSEP>[argument 1; litteral](str){two.sided}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){N}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sample}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){N}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){presp}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){prespT}<LSEP>[](symbol){prespC}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){se.rr.alt.T}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){prespT}<LEND>[](symbol){se}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){se.rr.alt.C}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){prespC}<LEND>[](symbol){se}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){se}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.alt.T}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.alt.C}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){presp.null}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){prespT.null}<LSEP>[](symbol){prespC.null}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){se.rr.null.T}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){prespT.null}<LEND>[](symbol){se}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){se.rr.null.C}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){se.f.rr}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){sample}<LSEP>[](symbol){r}<LSEP>[](symbol){prespC.null}<LEND>[](symbol){se}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){se.null}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.null.T}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){se.rr.null.C}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){thld.low}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sig.level}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){se.null}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){thld.high}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){presp.null}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sig.level}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){se.null}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){power.low}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.low}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){power.high}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){thld.high}<LSEP>[](symbol){presp}<LSEP>[](symbol){se}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){power.n}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){power.low}<LSEP>[](symbol){power.high}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){power}<LSEP>[](symbol){power.n}<LEND>[argument 1; litteral](real){0.010000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){N}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){break}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){sample}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){N}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Your n exceeds 100,000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){return.object}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){design}<LSEP>[](symbol){n}<LSEP>[](symbol){r}<LSEP>[](symbol){presp}<LSEP>[](symbol){presp.null}<LSEP>[](symbol){sig.level}<LSEP>[](symbol){power}<LSEP>[](symbol){type}<LSEP>[](symbol){alternative}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){return.object}<LEND>[assign](){<-}<LSEP>[](symbol){power.rr.plot}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){design}<LSEP>[](symbol){n.seq}<LSEP>[](symbol){r}<LSEP>[](symbol){presp.seq}<LSEP>[](symbol){presp.null}<LSEP>[](symbol){sig.level}<LSEP>[](symbol){prespT.seq}<LSEP>[](symbol){prespC.seq}<LSEP>[](symbol){prespT.null}<LSEP>[](symbol){prespC.null}<LSEP>[](symbol){type}<LSEP>[](symbol){alternative}<LSEP>[](symbol){solve.tolerance}<LSEP>[](symbol){legend}<LSEP>[](symbol){legend.x}<LSEP>[](symbol){legend.y}<LSEP>[](symbol){par}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){n.seq}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Please provide a vector of sam...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){presp.seq}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Please provide a vector of pro...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){power}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){presp.null}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){presp.null}<LSEP>[litteral](NULL){NULL}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){prespT.null}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){prespT.null}<LSEP>[litteral](NULL){NULL}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){alternative}<LSEP>[argument 1; litteral](str){one.sided}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){alt}<LSEP>[litteral](str){One Sided}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){alt}<LSEP>[litteral](str){Two Sided}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){one.sample}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){n}<LSEP>[](symbol){n.seq}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){power}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){presp.seq}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){presp.seq}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){power}<LSEP>[](symbol){n}<LEND>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){power.rr.test}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){n}<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){presp.seq}<LSEP>[](symbol){i}<LEND>[](symbol){presp.null}<LSEP>[](symbol){design}<LSEP>[](symbol){sig.level}<LSEP>[](symbol){type}<LSEP>[](symbol){alternative}<LEND>[](symbol){power}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){prespT.seq}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){prespC.seq}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){length of vector prespT.seq is...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){presp.seq}<LSEP>[](symbol){prespT.seq}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){n}<LSEP>[](symbol){n.seq}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){power}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){presp.seq}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){presp.seq}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){power}<LSEP>[](symbol){n}<LEND>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){power.rr.test}<LSEP>[](symbol){p}<LSEP>[](symbol){p0}<LSEP>[](symbol){p1}<LSEP>[](symbol){q}<LSEP>[](symbol){n}<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){presp.seq}<LSEP>[](symbol){i}<LEND>[argument 6; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){prespC.seq}<LSEP>[](symbol){i}<LEND>[](symbol){prespT.null}<LSEP>[](symbol){prespC.null}<LSEP>[](symbol){design}<LSEP>[](symbol){sig.level}<LSEP>[](symbol){type}<LSEP>[](symbol){alternative}<LEND>[](symbol){power}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){par}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){3.600000}<LSEP>[argument 1; litteral](real){3.600000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){0.700000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.010000}<LEND>[argument 5; litteral](real){0.800000}<LEND>[statement 8; call](){}<LSEP>[](symbol){plot}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](str){n}<LEND>[argument 3; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){presp.seq}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1.050000}<LEND>[](symbol){F}<LSEP>[argument 6; litteral](str){}<LSEP>[argument 7; litteral](str){}<LEND>[statement 9; call](){}<LSEP>[](symbol){abline}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](str){dashed}<LSEP>[argument 2; litteral](str){darkgray}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){col.seq}<LEND>[call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){gray}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){n.seq}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){3000.000000}<LSEP>[argument 1; litteral](real){150.000000}<LEND>[statement 11; control flow](){for}<LSEP>[](symbol){n}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){n.seq}<LEND>[body; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){presp.seq}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){power}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){n.seq}<LSEP>[](symbol){n}<LEND>[argument 2; litteral](real){1.500000}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){col.seq}<LSEP>[](symbol){n}<LEND>[statement 12; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 13; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[statement 14; call](){}<LSEP>[](symbol){mtext}<LSEP>[argument 0; litteral](str){Population Proportion of Respo...}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){2.500000}<LSEP>[argument 4; litteral](real){0.800000}<LEND>[statement 15; call](){}<LSEP>[](symbol){mtext}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Statistical Power for}<LSEP>[](symbol){alt}<LSEP>[argument 2; litteral](str){Test}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){2.500000}<LSEP>[argument 4; litteral](real){0.800000}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){legend}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){legend}<LSEP>[](symbol){legend.x}<LSEP>[](symbol){legend.y}<LSEP>[](symbol){n.seq}<LSEP>[argument 3; litteral](str){Sample size}<LSEP>[argument 4; litteral](real){1.000000}<LSEP>[](symbol){col.seq}<LSEP>[argument 6; litteral](str){n}<LSEP>[argument 7; litteral](real){0.800000}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){as.data.frame.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){row.names}<LSEP>[](symbol){optional}<LSEP>[](symbol){...}<LSEP>[](symbol){group.name}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fold}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){name.fold}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){fold}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){name.fold}<LSEP>[argument 1; litteral](str){is not of class 'folder'.}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fold}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fold}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){g}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){g}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){n}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){g}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fold}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){g}<LSEP>[](symbol){n}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[](symbol){group.name}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}

[](){expression}<LSEP>[litteral](NULL){NULL}

[](){expression}<LSEP>[call](){}<LSEP>[](symbol){setGeneric}<LSEP>[argument 0; litteral](str){map}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LEND>[call](){}<LSEP>[](symbol){setMethod}<LSEP>[argument 0; litteral](str){map}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){ANY}<LSEP>[argument 1; litteral](str){formula}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){map}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.function}<LSEP>[](symbol){f}<LEND>[](symbol){...}<LEND>[call](){}<LSEP>[](symbol){setMethod}<LSEP>[argument 0; litteral](str){map}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){atomic}<LSEP>[argument 1; litteral](str){function}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){map}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.list}<LSEP>[](symbol){x}<LEND>[](symbol){f}<LSEP>[](symbol){...}<LEND>[call](){}<LSEP>[](symbol){setMethod}<LSEP>[argument 0; litteral](str){map}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){list}<LSEP>[argument 1; litteral](str){function}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){p}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){mapList}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){p}<LSEP>[](symbol){...}<LEND>[call](){}<LSEP>[](symbol){%g%}<LEND>[argument 0; call](){}<LSEP>[](symbol){mapList}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){p}<LSEP>[](symbol){...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){standardGeneric}<LSEP>[argument 0; litteral](str){mapList}<LEND>[call](){}<LSEP>[](symbol){%m%}<LEND>[argument 0; call](){}<LSEP>[](symbol){mapList}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){x}<LSEP>[](symbol){list}<LEND>[argument 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){function}<LEND>[argument 2; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){p}<LSEP>[](symbol){formula}<LEND>[](symbol){...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){mapList}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LEND>[argument 2; call](){}<LSEP>[](symbol){as.function}<LSEP>[](symbol){p}<LEND>[](symbol){...}<LEND>[call](){}<LSEP>[](symbol){%m%}<LEND>[argument 0; call](){}<LSEP>[](symbol){mapList}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){x}<LSEP>[](symbol){list}<LEND>[argument 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){function}<LEND>[argument 2; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](str){function}<LEND>[](symbol){...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ind}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){x}<LSEP>[](symbol){p}<LEND>[argument 2; call](){}<LSEP>[](symbol){logical}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){mapListOnIndex}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){ind}<LSEP>[](symbol){...}<LEND>[call](){}<LSEP>[](symbol){%m%}<LEND>[argument 0; call](){}<LSEP>[](symbol){mapList}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){x}<LSEP>[](symbol){list}<LEND>[argument 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){function}<LEND>[argument 2; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){p}<LSEP>[](symbol){character}<LEND>[](symbol){...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ind}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){^\\^}<LSEP>[](symbol){p}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[](symbol){p}<LEND>[statement 1; call](){}<LSEP>[](symbol){mapListOnIndex}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){ind}<LSEP>[](symbol){...}<LEND>[assign](){<-}<LSEP>[](symbol){mapListOnIndex}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){ind}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){memClassHandler}<LEND>[call](){}<LSEP>[](symbol){MemClassHandler}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){memClassHandler}<LSEP>[](symbol){memClass}<LEND>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){ind}<LEND>[call](){}<LSEP>[](symbol){verboseApply}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.list}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){ind}<LEND>[](symbol){f}<LSEP>[](symbol){...}<LEND>[statement 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){memClassHandler}<LSEP>[](symbol){wrapClass}<LEND>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){setClassUnion}<LSEP>[argument 0; litteral](str){numericORcharacteORlogical}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){numeric}<LSEP>[argument 1; litteral](str){character}<LSEP>[argument 2; litteral](str){logical}<LEND>[call](){}<LSEP>[](symbol){setMethod}<LSEP>[argument 0; litteral](str){map}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){list}<LSEP>[argument 1; litteral](str){numericORcharacteORlogical}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){force}<LSEP>[](symbol){f}<LEND>[statement 1; call](){}<LSEP>[](symbol){map}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){.}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){.}<LSEP>[](symbol){f}<LEND>[](symbol){...}<LEND>[call](){}<LSEP>[](symbol){setMethod}<LSEP>[argument 0; litteral](str){map}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){MList}<LSEP>[argument 1; litteral](str){function}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LSEP>[](symbol){simplify}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){localmc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){do.call}<LSEP>[](symbol){mcmapply}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){f}<LEND>[](symbol){x}<LSEP>[](symbol){simplify}<LSEP>[](symbol){...}<LEND>[statement 1; call](){}<LSEP>[](symbol){verboseApply}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LSEP>[](symbol){localmc}<LEND>[call](){}<LSEP>[](symbol){setMethod}<LSEP>[argument 0; litteral](str){map}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){formula}<LSEP>[argument 1; litteral](str){function}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mlist}<LEND>[call](){}<LSEP>[](symbol){eval}<LEND>[argument 0; call](){}<LSEP>[](symbol){parse}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){list(}<LEND>[argument 1; call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){~}<LSEP>[argument 1; litteral](str){,}<LEND>[argument 2; call](){}<LSEP>[](symbol){deparse}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){)}<LEND>[argument 1; call](){}<LSEP>[](symbol){environment}<LSEP>[](symbol){x}<LEND>[statement 1; call](){}<LSEP>[](symbol){map}<LEND>[argument 0; call](){}<LSEP>[](symbol){do.call}<LSEP>[](symbol){MList}<LSEP>[](symbol){mlist}<LEND>[](symbol){f}<LSEP>[](symbol){...}<LEND>[call](){}<LSEP>[](symbol){setGeneric}<LSEP>[argument 0; litteral](str){flatmap}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LSEP>[](symbol){flatten}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){as.function}<LSEP>[](symbol){flatten}<LEND>[argument 0; call](){}<LSEP>[](symbol){map}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LEND>[call](){}<LSEP>[](symbol){setMethod}<LSEP>[argument 0; litteral](str){flatmap}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){ANY}<LSEP>[argument 1; litteral](str){formula}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LSEP>[](symbol){flatten}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){flatmap}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.function}<LSEP>[](symbol){f}<LEND>[](symbol){...}<LSEP>[](symbol){flatten}<LEND>[call](){}<LSEP>[](symbol){setGeneric}<LSEP>[argument 0; litteral](str){sac}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){by}<LSEP>[](symbol){...}<LSEP>[](symbol){combine}<LEND>[body; call](){}<LSEP>[](symbol){standardGeneric}<LSEP>[argument 0; litteral](str){sac}<LEND>[call](){}<LSEP>[](symbol){setMethod}<LSEP>[argument 0; litteral](str){sac}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){data.frame}<LSEP>[argument 1; litteral](str){function}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){by}<LSEP>[](symbol){...}<LSEP>[](symbol){combine}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){indList}<LEND>[call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){extract}<LSEP>[](symbol){x}<LSEP>[](symbol){by}<LEND>[statement 1; call](){}<LSEP>[](symbol){flatmap}<LSEP>[](symbol){indList}<LEND>[argument 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){ind}<LEND>[argument 1; call](){}<LSEP>[](symbol){f}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){ind}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[](symbol){...}<LEND>[](symbol){combine}<LEND>[call](){}<LSEP>[](symbol){setMethod}<LSEP>[argument 0; litteral](str){sac}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){ANY}<LSEP>[argument 1; litteral](str){formula}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){by}<LSEP>[](symbol){...}<LSEP>[](symbol){combine}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){sac}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.function}<LSEP>[](symbol){f}<LEND>[](symbol){by}<LSEP>[](symbol){...}<LSEP>[](symbol){combine}<LEND>[assign](){<-}<LSEP>[](symbol){vmap}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LSEP>[](symbol){.mc}<LSEP>[](symbol){.bar}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){map}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LSEP>[](symbol){.mc}<LSEP>[](symbol){.bar}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){WC_FST_FiniteSample_Haploids_2AllelesB_MCW}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){AllCounts}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n_pops}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){AllCounts}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){r}<LSEP>[](symbol){n_pops}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){counts1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){AllCounts}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){sample_sizes}<LEND>[call](){}<LSEP>[](symbol){rowSums}<LSEP>[](symbol){AllCounts}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){n_ave}<LEND>[call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){sample_sizes}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){n_c}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_pops}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){sample_sizes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_pops}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_pops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){p_freqs}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){counts1}<LSEP>[](symbol){sample_sizes}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){p_ave}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LSEP>[](symbol){p_freqs}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_pops}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){He}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){s2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p_freqs}<LSEP>[](symbol){p_ave}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_pops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n_ave}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){T1}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){s2}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_ave}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){s2}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){r}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){T2}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_c}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_ave}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_c}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_ave}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){s2}<LEND>[](symbol){r}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){FST}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){T1}<LSEP>[](symbol){T2}<LEND>[statement 13; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){He}<LSEP>[](symbol){p_ave}<LSEP>[](symbol){FST}<LSEP>[](symbol){T1}<LSEP>[](symbol){T2}<LEND>[assign](){<-}<LSEP>[](symbol){WC_FST_FiniteSample_Haploids_2AllelesB_NoSamplingCorrection}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){AllCounts}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n_pops}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){AllCounts}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){r}<LSEP>[](symbol){n_pops}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){counts1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){AllCounts}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){sample_sizes}<LEND>[call](){}<LSEP>[](symbol){rowSums}<LSEP>[](symbol){AllCounts}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){n_ave}<LEND>[call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){sample_sizes}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){n_c}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_pops}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){sample_sizes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_pops}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_pops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){p_freqs}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){counts1}<LSEP>[](symbol){sample_sizes}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){p_ave}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LSEP>[](symbol){p_freqs}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_pops}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){He}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){s2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p_freqs}<LSEP>[](symbol){p_ave}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_pops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n_ave}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){T1NoCorr}<LSEP>[](symbol){s2}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){T2NoCorr}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){s2}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){FSTNoCorr}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){T1NoCorr}<LSEP>[](symbol){T2NoCorr}<LEND>[statement 13; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){He}<LSEP>[](symbol){p_ave}<LSEP>[](symbol){FSTNoCorr}<LSEP>[](symbol){T1NoCorr}<LSEP>[](symbol){T2NoCorr}<LEND>[assign](){=}<LSEP>[](symbol){fstBarCalculatorNoCorr}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){DataList}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataList}<LSEP>[](symbol){T1NoCorr}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataList}<LSEP>[](symbol){OutlierFlag}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataList}<LSEP>[](symbol){T2NoCorr}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataList}<LSEP>[](symbol){OutlierFlag}<LEND>[assign](){=}<LSEP>[](symbol){fstBarCalculator}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){DataList}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataList}<LSEP>[](symbol){T1}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataList}<LSEP>[](symbol){OutlierFlag}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataList}<LSEP>[](symbol){T2}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataList}<LSEP>[](symbol){OutlierFlag}<LEND>[assign](){<-}<LSEP>[](symbol){WC_FST_FiniteSample_Diploids_2Alleles_NoCorr}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Sample_Mat}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){sample_sizes}<LEND>[call](){}<LSEP>[](symbol){rowSums}<LSEP>[](symbol){Sample_Mat}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){n_ave}<LEND>[call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){sample_sizes}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){n_pops}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){Sample_Mat}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){r}<LSEP>[](symbol){n_pops}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){n_c}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_pops}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){sample_sizes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_pops}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_pops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){p_freqs}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sample_Mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sample_Mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){sample_sizes}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){p_ave}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LSEP>[](symbol){p_freqs}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_pops}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){s2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p_freqs}<LSEP>[](symbol){p_ave}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_pops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n_ave}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){s2}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){h_freqs}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sample_Mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){sample_sizes}<LEND>[statement 10; assign](){=}<LSEP>[](symbol){h_ave}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LSEP>[](symbol){h_freqs}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_pops}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_c}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){s2}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){r}<LEND>[](symbol){s2}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){n_ave}<LEND>[](symbol){h_ave}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){h_ave}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){He}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){p_ave}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){FST}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){a}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){a}<LSEP>[](symbol){b}<LEND>[](symbol){c}<LEND>[statement 16; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){He}<LSEP>[](symbol){FST}<LSEP>[](symbol){a}<LEND>[argument 3; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){a}<LSEP>[](symbol){b}<LEND>[](symbol){c}<LEND>[assign](){<-}<LSEP>[](symbol){WC_FST_FiniteSample_Diploids_2Alleles}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Sample_Mat}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){sample_sizes}<LEND>[call](){}<LSEP>[](symbol){rowSums}<LSEP>[](symbol){Sample_Mat}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){n_ave}<LEND>[call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){sample_sizes}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){n_pops}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){Sample_Mat}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){r}<LSEP>[](symbol){n_pops}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){n_c}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_pops}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){sample_sizes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_pops}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_pops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){p_freqs}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sample_Mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sample_Mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){sample_sizes}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){p_ave}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LSEP>[](symbol){p_freqs}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_pops}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){s2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p_freqs}<LSEP>[](symbol){p_ave}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_pops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n_ave}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){s2}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){h_freqs}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sample_Mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){sample_sizes}<LEND>[statement 10; assign](){=}<LSEP>[](symbol){h_ave}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LSEP>[](symbol){h_freqs}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_pops}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_c}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){s2}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_ave}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){r}<LEND>[](symbol){s2}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](symbol){h_ave}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_ave}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){r}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){r}<LEND>[](symbol){s2}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n_ave}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){n_ave}<LEND>[](symbol){h_ave}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){h_ave}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){He}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){p_ave}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){FST}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){a}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){a}<LSEP>[](symbol){b}<LEND>[](symbol){c}<LEND>[statement 16; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){He}<LSEP>[](symbol){FST}<LSEP>[](symbol){a}<LEND>[argument 3; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){a}<LSEP>[](symbol){b}<LEND>[](symbol){c}

[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){mvdct}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){variant}<LSEP>[](symbol){inverted}<LEND>[body; call](){}<LSEP>[](symbol){mvdtt}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){dct}<LSEP>[](symbol){variant}<LSEP>[](symbol){inverted}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gompertz_new}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){w}<LSEP>[](symbol){start}<LSEP>[](symbol){max_iter}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){upper_bound}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){start}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){start}<LEND>[argument 1; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'start' must be of length 4}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){start}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){start}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){parameter 'beta' cannot be sma...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){start}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){parameter 'eta' cannot be init...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){object}<LEND>[call](){}<LSEP>[](symbol){structure}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){w}<LEND>[argument 3; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[argument 4; call](){}<LSEP>[](symbol){suff_stats}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){w}<LEND>[argument 5; litteral](logical){FALSE}<LSEP>[](symbol){start}<LSEP>[](symbol){max_iter}<LEND>[argument 1; litteral](str){gompertz}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){lower_bound}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){upper_bound}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){constrained}<LEND>[litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){lower_bound}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){inf}<LEND>[argument 1; litteral](real){4.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lower_bound}<LEND>[argument 1; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'lower_bound' must be of length 4}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lower_bound}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lower_bound}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lower_bound}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lower_bound}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){upper_bound}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){inf}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){upper_bound}<LEND>[argument 1; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'upper_bound' must be of length 4}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upper_bound}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upper_bound}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upper_bound}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upper_bound}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[](symbol){lower_bound}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[](symbol){upper_bound}<LEND>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){gompertz_fn}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){alpha}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){beta}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){phi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){alpha}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){beta}<LSEP>[](symbol){alpha}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){eta}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[](symbol){phi}<LEND>[assign](){<-}<LSEP>[](symbol){fn.gompertz}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){gompertz_fn}<LSEP>[](symbol){x}<LSEP>[](symbol){theta}<LEND>[assign](){<-}<LSEP>[](symbol){fn.gompertz_fit}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){gompertz_fn}<LSEP>[](symbol){x}<LSEP>[](symbol){theta}<LEND>[assign](){<-}<LSEP>[](symbol){gradient_hessian.gompertz}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){alpha}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){beta}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){phi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){omega}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){beta}<LSEP>[](symbol){alpha}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){eta}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[](symbol){phi}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){b}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[](symbol){phi}<LEND>[](symbol){b}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){eta}<LEND>[](symbol){b}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LSEP>[](symbol){g}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){u}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LSEP>[](symbol){g}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){v}<LEND>[call](){}<LSEP>[](symbol){expm1}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){eta}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[](symbol){phi}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){gradient}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){m}<LEND>[argument 2; litteral](real){4.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){hessian}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){m}<LEND>[argument 1; litteral](real){4.000000}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gradient}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){g}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gradient}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){g}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gradient}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){omega}<LSEP>[](symbol){t}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gradient}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){omega}<LSEP>[](symbol){u}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[litteral](real){0.000000}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[litteral](real){0.000000}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){t}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){u}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[litteral](real){0.000000}<LEND>[statement 24; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[litteral](real){0.000000}<LEND>[statement 25; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[](symbol){t}<LEND>[statement 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[](symbol){u}<LEND>[statement 27; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 28; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[statement 29; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){omega}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[](symbol){phi}<LEND>[](symbol){t}<LEND>[](symbol){v}<LEND>[statement 30; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){omega}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){u}<LSEP>[](symbol){eta}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){eta}<LSEP>[](symbol){t}<LEND>[](symbol){v}<LEND>[statement 31; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 32; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[statement 33; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[statement 34; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){omega}<LEND>[](symbol){eta}<LEND>[](symbol){u}<LEND>[](symbol){v}<LEND>[statement 35; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){gradient}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gradient}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.nan}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gradient}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gradient}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.nan}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gradient}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[litteral](real){0.000000}<LEND>[statement 36; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){hessian}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){hessian}<LEND>[litteral](real){0.000000}<LEND>[statement 37; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){gradient}<LSEP>[](symbol){hessian}<LEND>[assign](){<-}<LSEP>[](symbol){rss.gompertz}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mu}<LEND>[call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){theta}<LEND>[statement 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[](symbol){mu}<LEND>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){rss_fixed.gompertz}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){known_param}<LEND>[body; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){z}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){idx}<LEND>[call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){known_param}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){theta}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[](symbol){idx}<LEND>[](symbol){z}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){idx}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){known_param}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){idx}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mu}<LEND>[call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){theta}<LEND>[statement 5; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[](symbol){mu}<LEND>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){rss_gradient_hessian.gompertz}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mu}<LEND>[call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){theta}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mu_gradient_hessian}<LEND>[call](){}<LSEP>[](symbol){gradient_hessian}<LSEP>[](symbol){object}<LSEP>[](symbol){theta}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){G}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mu_gradient_hessian}<LSEP>[](symbol){G}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){H}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mu_gradient_hessian}<LSEP>[](symbol){H}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){gradient}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){r}<LEND>[](symbol){G}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){hessian}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[argument 1; litteral](real){4.000000}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){G}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){G}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[](symbol){G}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[](symbol){G}<LEND>[statement 11; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){gradient}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sum}<LEND>[argument 1; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){hessian}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[](symbol){sum}<LEND>[assign](){<-}<LSEP>[](symbol){rss_gradient_hessian_fixed.gompertz}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){known_param}<LEND>[body; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){z}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){idx}<LEND>[call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){known_param}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){theta}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[](symbol){idx}<LEND>[](symbol){z}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){idx}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){known_param}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){idx}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mu}<LEND>[call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){theta}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){mu_gradient_hessian}<LEND>[call](){}<LSEP>[](symbol){gradient_hessian}<LSEP>[](symbol){object}<LSEP>[](symbol){theta}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){G}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mu_gradient_hessian}<LSEP>[](symbol){G}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){H}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mu_gradient_hessian}<LSEP>[](symbol){H}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){gradient}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){r}<LEND>[](symbol){G}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){hessian}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[argument 1; litteral](real){4.000000}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){G}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){G}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[](symbol){G}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[](symbol){G}<LEND>[statement 15; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gradient}<LSEP>[](symbol){}<LSEP>[](symbol){idx}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sum}<LEND>[argument 1; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hessian}<LSEP>[](symbol){}<LSEP>[](symbol){idx}<LSEP>[](symbol){idx}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[](symbol){sum}<LEND>[assign](){<-}<LSEP>[](symbol){mle_asy.gompertz}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){phi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){eta}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[](symbol){phi}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){t1}<LSEP>[litteral](real){0.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){t2}<LSEP>[litteral](real){0.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){t3}<LSEP>[litteral](real){0.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){t4}<LSEP>[litteral](real){0.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){t5}<LSEP>[litteral](real){0.000000}<LEND>[statement 12; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){t1}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){t1}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){g}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){g}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){t2}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){t2}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){g}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){t3}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){t3}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){g}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){t4}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){t4}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){g}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){t5}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){t5}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){g}<LSEP>[](symbol){i}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){denom}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){t1}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){t2}<LSEP>[](symbol){t3}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){denom}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){alpha}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){t1}<LSEP>[](symbol){t5}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){t3}<LSEP>[](symbol){t4}<LEND>[](symbol){denom}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){beta}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){t1}<LSEP>[](symbol){t4}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){t2}<LSEP>[](symbol){t5}<LEND>[](symbol){denom}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){beta}<LSEP>[](symbol){alpha}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){alpha}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){beta}<LEND>[](symbol){theta}<LEND>[assign](){<-}<LSEP>[](symbol){init.gompertz}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){stats}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rss_fn}<LEND>[call](){}<LSEP>[](symbol){rss}<LSEP>[](symbol){object}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){linear_fit}<LEND>[call](){}<LSEP>[](symbol){summary}<LEND>[argument 0; call](){}<LSEP>[](symbol){lm}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){linear_coef}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){linear_fit}<LSEP>[](symbol){coefficients}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){min_value}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){max_value}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){zv}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[](symbol){min_value}<LEND>[argument 1; litteral](real){0.000010}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){max_value}<LSEP>[](symbol){min_value}<LEND>[argument 1; litteral](real){0.000020}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){zv}<LEND>[call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){zv}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){lm}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){zv}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){coefficients}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){phi}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){coefficients}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){eta}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){theta}<LEND>[call](){}<LSEP>[](symbol){mle_asy}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){min_value}<LSEP>[](symbol){max_value}<LSEP>[](symbol){eta}<LSEP>[](symbol){phi}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){best_rss}<LEND>[call](){}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){theta}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){niter}<LSEP>[litteral](real){1.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){linear_coef}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; litteral](real){0.200000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){weighted_mean}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){w}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){theta}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){0.900000}<LSEP>[](symbol){weighted_mean}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[](symbol){min_value}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){0.900000}<LSEP>[](symbol){weighted_mean}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[](symbol){max_value}<LEND>[argument 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){linear_coef}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.001000}<LEND>[false branch; litteral](real){0.001000}<LEND>[argument 3; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){m}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){best_rss}<LEND>[call](){}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){theta}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){delta}<LEND>[call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){v1}<LSEP>[litteral](integer){20}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){v2}<LSEP>[litteral](integer){20}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){v}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){v1}<LSEP>[](symbol){v2}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){eta_set}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){5.000000}<LEND>[argument 1; litteral](real){5.000000}<LSEP>[](symbol){v1}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){phi_set}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){delta}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){m}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){delta}<LEND>[](symbol){v2}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){theta_tmp}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){v}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){rss_tmp}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){10000.000000}<LSEP>[](symbol){v}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){theta_eta_1}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){v2}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){rss_eta_1}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){10000.000000}<LSEP>[](symbol){v2}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){theta_eta_2}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){v2}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){rss_eta_2}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){10000.000000}<LSEP>[](symbol){v2}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){i}<LSEP>[litteral](real){0.000000}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){j}<LSEP>[litteral](real){0.000000}<LEND>[statement 30; control flow](){for}<LSEP>[](symbol){phi}<LSEP>[](symbol){phi_set}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){eta}<LSEP>[](symbol){eta_set}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){current_par}<LEND>[call](){}<LSEP>[](symbol){mle_asy}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){eta}<LSEP>[](symbol){phi}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){current_rss}<LEND>[call](){}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){current_par}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta_tmp}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[](symbol){current_par}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rss_tmp}<LSEP>[](symbol){i}<LEND>[](symbol){current_rss}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){current_par}<LEND>[call](){}<LSEP>[](symbol){mle_asy}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){20.000000}<LEND>[](symbol){phi}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){current_rss}<LEND>[call](){}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){current_par}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta_eta_1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[](symbol){current_par}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rss_eta_1}<LSEP>[](symbol){j}<LEND>[](symbol){current_rss}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){current_par}<LEND>[call](){}<LSEP>[](symbol){mle_asy}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](real){20.000000}<LSEP>[](symbol){phi}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){current_rss}<LEND>[call](){}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){current_par}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta_eta_2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[](symbol){current_par}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rss_eta_2}<LSEP>[](symbol){j}<LEND>[](symbol){current_rss}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){ord}<LEND>[call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){rss_tmp}<LEND>[statement 32; assign](){<-}<LSEP>[](symbol){theta_1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta_tmp}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ord}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){theta_2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta_tmp}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ord}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){v}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 34; assign](){<-}<LSEP>[](symbol){theta_3}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta_tmp}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ord}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){v}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 35; assign](){<-}<LSEP>[](symbol){theta_4}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta_eta_1}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){rss_eta_1}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 36; assign](){<-}<LSEP>[](symbol){theta_5}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta_eta_2}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){rss_eta_2}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 37; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){constrained}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){theta}<LEND>[call](){}<LSEP>[](symbol){pmax}<LEND>[argument 0; call](){}<LSEP>[](symbol){pmin}<LSEP>[](symbol){theta}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){theta_1}<LEND>[call](){}<LSEP>[](symbol){pmax}<LEND>[argument 0; call](){}<LSEP>[](symbol){pmin}<LSEP>[](symbol){theta_1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){theta_2}<LEND>[call](){}<LSEP>[](symbol){pmax}<LEND>[argument 0; call](){}<LSEP>[](symbol){pmin}<LSEP>[](symbol){theta_2}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){theta_3}<LEND>[call](){}<LSEP>[](symbol){pmax}<LEND>[argument 0; call](){}<LSEP>[](symbol){pmin}<LSEP>[](symbol){theta_3}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){theta_4}<LEND>[call](){}<LSEP>[](symbol){pmax}<LEND>[argument 0; call](){}<LSEP>[](symbol){pmin}<LSEP>[](symbol){theta_4}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){theta_5}<LEND>[call](){}<LSEP>[](symbol){pmax}<LEND>[argument 0; call](){}<LSEP>[](symbol){pmin}<LSEP>[](symbol){theta_5}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 38; assign](){<-}<LSEP>[](symbol){start}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){theta}<LSEP>[](symbol){theta_1}<LSEP>[](symbol){theta_2}<LSEP>[](symbol){theta_3}<LSEP>[](symbol){theta_4}<LSEP>[](symbol){theta_5}<LEND>[statement 39; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){fit_nlminb}<LSEP>[](symbol){object}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){start}<LEND>[statement 40; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.infinite}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){rss}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){rss}<LEND>[](symbol){best_rss}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){theta}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){theta}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){best_rss}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){rss}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){niter}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){niter}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){niter}<LEND>[statement 41; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){theta}<LEND>[litteral](NULL){NULL}<LEND>[statement 42; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){niter}<LEND>[litteral](NULL){NULL}<LEND>[statement 43; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){tmp}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 44; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){theta}<LSEP>[](symbol){niter}<LEND>[assign](){<-}<LSEP>[](symbol){fit.gompertz}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){solution}<LEND>[call](){}<LSEP>[](symbol){find_optimum}<LSEP>[](symbol){object}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){theta}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){optimum}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){converged}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){iterations}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[argument 3; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){TRUE}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](symbol){theta}<LEND>[argument 5; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){minimum}<LEND>[argument 6; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){n}<LEND>[argument 1; litteral](real){4.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){gompertz_fn}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[](symbol){theta}<LEND>[argument 8; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){w}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){residuals}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){fitted.values}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){param_names}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){alpha}<LSEP>[argument 1; litteral](str){beta}<LSEP>[argument 2; litteral](str){eta}<LSEP>[argument 3; litteral](str){phi}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){coefficients}<LEND>[](symbol){param_names}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){estimated}<LEND>[](symbol){param_names}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){result}<LEND>[litteral](str){gompertz_fit}<LEND>[](symbol){result}<LEND>[assign](){<-}<LSEP>[](symbol){fit_constrained.gompertz}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){constraint}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){FALSE}<LSEP>[argument 1; litteral](real){4.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){seq_len}<LSEP>[argument 0; litteral](real){4.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lb_is_inf}<LEND>[call](){}<LSEP>[](symbol){is.infinite}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ub_is_inf}<LEND>[call](){}<LSEP>[](symbol){is.infinite}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[](symbol){i}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){constraint}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[litteral](logical){TRUE}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){lb_is_inf}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){ub_is_inf}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){constraint}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){constraint}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){known_param}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){constraint}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[argument 2; litteral](real){nan}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){solution}<LEND>[call](){}<LSEP>[](symbol){find_optimum_constrained}<LSEP>[](symbol){object}<LSEP>[](symbol){constraint}<LSEP>[](symbol){known_param}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){theta}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){constraint}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){optimum}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){estimated}<LEND>[call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){constraint}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){converged}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){iterations}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){constraint}<LSEP>[](symbol){estimated}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){estimated}<LSEP>[](symbol){theta}<LEND>[argument 5; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){minimum}<LEND>[argument 6; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){estimated}<LEND>[argument 7; call](){}<LSEP>[](symbol){gompertz_fn}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[](symbol){theta}<LEND>[argument 8; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){w}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){residuals}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){fitted.values}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){param_names}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){alpha}<LSEP>[argument 1; litteral](str){beta}<LSEP>[argument 2; litteral](str){eta}<LSEP>[argument 3; litteral](str){phi}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){coefficients}<LEND>[](symbol){param_names}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){estimated}<LEND>[](symbol){param_names}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){result}<LEND>[litteral](str){gompertz_fit}<LEND>[](symbol){result}<LEND>[assign](){<-}<LSEP>[](symbol){fisher_info.gompertz}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){theta}<LSEP>[](symbol){sigma}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){theta}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){stats}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){gh}<LEND>[call](){}<LSEP>[](symbol){gradient_hessian}<LSEP>[](symbol){object}<LSEP>[](symbol){theta}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){G}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){m}<LEND>[argument 2; litteral](real){4.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){G}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){G}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sum}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){H}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){m}<LEND>[argument 1; litteral](real){4.000000}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){H}<LEND>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){H}<LEND>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){H}<LEND>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){H}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){H}<LEND>[](symbol){}<LSEP>[](symbol){}<LSEP>[argument 3; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gh}<LSEP>[](symbol){G}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){H}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){H}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[](symbol){sum}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){mu}<LEND>[call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[](symbol){theta}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){y}<LEND>[](symbol){mu}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){sigma}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){n}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){fim}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){H}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[](symbol){G}<LEND>[](symbol){sigma}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[](symbol){G}<LEND>[](symbol){sigma}<LEND>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){sigma}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){lab}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){theta}<LEND>[argument 1; litteral](str){sigma}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){fim}<LEND>[](symbol){lab}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){fim}<LEND>[](symbol){lab}<LEND>[](symbol){fim}<LEND>[assign](){<-}<LSEP>[](symbol){curve_variance.gompertz_fit}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){V}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){vcov}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){V}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){nan}<LSEP>[](symbol){m}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){alpha}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){beta}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){phi}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){omega}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){beta}<LSEP>[](symbol){alpha}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){eta}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[](symbol){phi}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){b}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LSEP>[](symbol){phi}<LEND>[](symbol){b}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){eta}<LEND>[](symbol){b}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){s}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LSEP>[](symbol){s}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){u}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LSEP>[](symbol){s}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){G}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){m}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){b}<LSEP>[](symbol){f}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){f}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){omega}<LSEP>[](symbol){t}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){omega}<LSEP>[](symbol){u}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){G}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.nan}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.nan}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[litteral](real){0.000000}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){variance}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){nan}<LSEP>[](symbol){m}<LEND>[statement 22; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){variance}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){tcrossprod}<LEND>[argument 0; call](){}<LSEP>[](symbol){crossprod}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[](symbol){V}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){G}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[](symbol){variance}<LEND>[assign](){<-}<LSEP>[](symbol){nauc.gompertz_fit}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){xlim}<LSEP>[](symbol){ylim}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){xlim}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'xlim' must be of length 2}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){xlim}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'xlim' must be a numeric vecto...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'xlim[1]' cannot be larger or ...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ylim}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'ylim' must be of length 2}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){ylim}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'ylim' must be a numeric vecto...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'ylim[1]' cannot be larger or ...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'ylim[1]' cannot be negative}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){alpha}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){beta}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){phi}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){I}<LSEP>[litteral](real){0.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){xlim_new}<LSEP>[](symbol){xlim}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){alpha}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){phi}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){beta}<LSEP>[](symbol){alpha}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){alpha}<LEND>[](symbol){eta}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){eta}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){tmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim_new}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){tmp}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){tmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim_new}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){tmp}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){phi}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){beta}<LSEP>[](symbol){alpha}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){alpha}<LEND>[](symbol){eta}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){eta}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){tmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){I}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){I}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){tmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim_new}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){tmp}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){tmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){I}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){I}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){tmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim_new}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){tmp}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){f}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[false branch; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){I}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){I}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){integrate}<LSEP>[](symbol){f}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim_new}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim_new}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){value}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){nauc}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){I}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){nauc}<LEND>[litteral](NULL){NULL}<LEND>[](symbol){nauc}<LEND>[assign](){<-}<LSEP>[](symbol){naac.gompertz_fit}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){xlim}<LSEP>[](symbol){ylim}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nauc}<LSEP>[](symbol){object}<LSEP>[](symbol){xlim}<LSEP>[](symbol){ylim}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plotframes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){xlab}<LSEP>[](symbol){ylab}<LSEP>[](symbol){font.size}<LSEP>[](symbol){layout}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){correl}<LEND>[call](){}<LSEP>[](symbol){cor}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){stack}<LSEP>[](symbol){x}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[](symbol){xx}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){groupe}<LSEP>[argument 1; litteral](str){xv}<LSEP>[argument 2; litteral](str){varx}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){yy}<LEND>[call](){}<LSEP>[](symbol){stack}<LSEP>[](symbol){y}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){yy}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){y}<LEND>[](symbol){yy}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){yy}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){groupe}<LSEP>[argument 1; litteral](str){yv}<LSEP>[argument 2; litteral](str){vary}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){xy}<LEND>[call](){}<LSEP>[](symbol){merge}<LSEP>[](symbol){xx}<LSEP>[](symbol){yy}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xy}<LSEP>[](symbol){groupe}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xy}<LSEP>[](symbol){groupe}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){levy}<LEND>[call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){y}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){nlevy}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){levy}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){ngraphy}<LEND>[call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){nlevy}<LSEP>[argument 1; litteral](real){9.000000}<LEND>[statement 14; control flow](){for}<LSEP>[](symbol){nx}<LEND>[range; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){iy}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ngraphy}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){jy}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){9.000000}<LSEP>[](symbol){iy}<LEND>[argument 1; litteral](real){8.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){jy}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){jy}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){jy}<LSEP>[argument 1; litteral](real){8.000000}<LEND>[](symbol){nlevy}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){xy.i}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xy}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xy}<LSEP>[](symbol){varx}<LEND>[](symbol){nx}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xy}<LSEP>[](symbol){vary}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levy}<LSEP>[](symbol){jy}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xy.i}<LSEP>[](symbol){vary}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xy.i}<LSEP>[](symbol){vary}<LEND>[argument 1; litteral](str){ (r = }<LEND>[argument 2; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){correl}<LSEP>[](symbol){nx}<LEND>[argument 2; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){xy.i}<LSEP>[](symbol){vary}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 3; litteral](str){)}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){graph.i}<LEND>[call](){}<LSEP>[](symbol){ggplot}<LSEP>[](symbol){xy.i}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes_q}<LEND>[argument 0; call](){}<LSEP>[](symbol){quote}<LSEP>[](symbol){xv}<LEND>[argument 1; call](){}<LSEP>[](symbol){quote}<LSEP>[](symbol){yv}<LEND>[argument 2; call](){}<LSEP>[](symbol){quote}<LSEP>[](symbol){groupe}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){graph.i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph.i}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_text}<LSEP>[argument 0; litteral](str){bold}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){graph.i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph.i}<LEND>[argument 1; call](){}<LSEP>[](symbol){facet_wrap}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){vary}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){free}<LEND>[argument 2; litteral](real){3.000000}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){xlab}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){xl}<LSEP>[](symbol){nx}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){xl}<LSEP>[](symbol){xlab}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ylab}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){yl}<LSEP>[litteral](str){}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){yl}<LSEP>[](symbol){ylab}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){graph.i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph.i}<LEND>[argument 1; call](){}<LSEP>[](symbol){labs}<LSEP>[](symbol){xl}<LSEP>[](symbol){yl}<LSEP>[](symbol){nx}<LEND>[statement 10; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){graph.i}<LEND>[statement 15; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.report.locmetric}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){metric}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence ...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: genlight object con...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){metric}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: name of the met...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){metric}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: metric is not n...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){field}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){metric}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){p1}<LEND>[assign](){<-}<LSEP>[](symbol){p2}<LSEP>[litteral](NULL){NULL}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){title1}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){SNP data - }<LSEP>[](symbol){metric}<LSEP>[argument 2; litteral](str){ by Locus}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){title1}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Fragment P/A data - }<LSEP>[](symbol){metric}<LSEP>[argument 2; litteral](str){ by Locus}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){metric_df}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){field}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){metric_df}<LEND>[litteral](str){field}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){p1}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ggplot}<LSEP>[](symbol){metric_df}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes}<LSEP>[](symbol){field}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_boxplot}<LEND>[argument 1; call](){}<LSEP>[](symbol){theme}<LEND>[argument 1; call](){}<LSEP>[](symbol){coord_flip}<LEND>[argument 1; call](){}<LSEP>[](symbol){ylab}<LSEP>[](symbol){metric}<LEND>[argument 1; call](){}<LSEP>[](symbol){ggtitle}<LSEP>[](symbol){title1}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){p2}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ggplot}<LSEP>[](symbol){metric_df}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes}<LSEP>[](symbol){field}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_histogram}<LSEP>[argument 0; litteral](real){50.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){xlab}<LSEP>[](symbol){metric}<LEND>[argument 1; call](){}<LSEP>[](symbol){ggtitle}<LSEP>[](symbol){title1}<LEND>[statement 17; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){gridExtra}<LSEP>[](symbol){grid.arrange}<LEND>[](symbol){p1}<LSEP>[](symbol){p2}<LEND>[statement 18; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Reporting}<LSEP>[](symbol){metric}<LSEP>[argument 2; litteral](str){Call Rate by Locus\n}<LEND>[statement 19; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of loci =}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 20; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of individuals =}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 21; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Minimum }<LSEP>[](symbol){metric}<LSEP>[argument 2; litteral](str){: }<LEND>[argument 3; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){metric_df}<LSEP>[](symbol){field}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 4; litteral](str){\n}<LEND>[statement 22; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Maximum }<LSEP>[](symbol){metric}<LSEP>[argument 2; litteral](str){: }<LEND>[argument 3; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){metric_df}<LSEP>[](symbol){field}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 4; litteral](str){\n}<LEND>[statement 23; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Average }<LSEP>[](symbol){metric}<LSEP>[argument 2; litteral](str){: }<LEND>[argument 3; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){metric_df}<LSEP>[](symbol){field}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 4; litteral](str){\n}<LEND>[statement 24; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Missing }<LSEP>[](symbol){metric}<LSEP>[argument 2; litteral](str){Overall : }<LEND>[argument 3; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 4; litteral](str){\n}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){percentile}<LEND>[call](){}<LSEP>[](symbol){quantile}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){metric_df}<LSEP>[](symbol){field}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){20.000000}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){retained}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){percentile}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){metric_df}<LSEP>[](symbol){field}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){metric_df}<LSEP>[](symbol){field}<LEND>[](symbol){y}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){pc.retained}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){retained}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){filtered}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[](symbol){retained}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){pc.filtered}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){100.000000}<LSEP>[](symbol){pc.retained}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){percentile}<LSEP>[](symbol){retained}<LSEP>[](symbol){pc.retained}<LSEP>[](symbol){filtered}<LSEP>[](symbol){pc.filtered}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){df}<LEND>[statement 32; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Threshold}<LSEP>[argument 1; litteral](str){Retained}<LSEP>[argument 2; litteral](str){Percent}<LSEP>[argument 3; litteral](str){Filtered}<LSEP>[argument 4; litteral](str){Percent}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Threshold}<LEND>[](symbol){}<LEND>[statement 34; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){df}<LEND>[litteral](NULL){NULL}<LEND>[statement 35; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 36; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){df}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rrat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){taus}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){rrat}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.report.diversity}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){gl}<LSEP>[](symbol){spectrumplot}<LSEP>[](symbol){confiplot}<LSEP>[](symbol){pbar}<LSEP>[](symbol){table}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LSEP>[](symbol){gl}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){gl}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Detected Presence/Absence (S...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Cannot calculate diversity ind...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){gl}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](str){all}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){gl}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){pops}<LEND>[call](){}<LSEP>[](symbol){seppop}<LSEP>[](symbol){gl}<LEND>[statement 10; control flow](){if}<LSEP>[](symbol){pbar}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pb}<LEND>[call](){}<LSEP>[](symbol){txtProgressBar}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){8.000000}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){20.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Counting missing loci... ...}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){nlocpop}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){pops}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[](symbol){T}<LEND>[statement 12; control flow](){if}<LSEP>[](symbol){pbar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){pb}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating zero_H/D_alpha .....}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){zero_H_alpha_es}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){pops}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dummys}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%%}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){dummys}<LSEP>[](symbol){T}<LEND>[argument 1; call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){dummys}<LSEP>[](symbol){T}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){dummys}<LSEP>[](symbol){T}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){dummys}<LSEP>[](symbol){T}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){zero_H_alpha}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){zero_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){zero_H_alpha_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){zero_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){zero_D_alpha}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){zero_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){zero_D_alpha_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){zero_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 18; control flow](){if}<LSEP>[](symbol){pbar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){pb}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating one_H/D_alpha ......}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){one_H_alpha_es}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){pops}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){logp}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.finite}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){p}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){log1_p}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.finite}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){dummys}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){logp}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){log1_p}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){dummys}<LEND>[argument 1; call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){dummys}<LEND>[argument 2; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){dummys}<LEND>[argument 3; call](){}<LSEP>[](symbol){sd}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){dummys}<LEND>[](symbol){dummys}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){one_H_alpha}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){one_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){one_H_alpha_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){one_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){one_D_alpha}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){one_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){one_D_alpha_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){one_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 24; control flow](){if}<LSEP>[](symbol){pbar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){pb}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating two_H/D_alpha ......}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){two_H_alpha_es}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){pops}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dummys}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){dummys}<LEND>[argument 1; call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){dummys}<LEND>[argument 2; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){dummys}<LEND>[argument 3; call](){}<LSEP>[](symbol){sd}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){dummys}<LEND>[](symbol){dummys}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){two_H_alpha}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){two_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){two_H_alpha_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){two_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){two_D_alpha}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){two_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){two_D_alpha_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){two_H_alpha_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){mat_zero_H_beta}<LSEP>[litteral](logical){NA}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){mat_one_H_beta}<LSEP>[litteral](logical){NA}<LEND>[statement 32; assign](){<-}<LSEP>[](symbol){mat_two_H_beta}<LSEP>[litteral](logical){NA}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){npops}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){pops}<LEND>[statement 34; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){npops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){pbar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){pb}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Counting pairwise missing loc...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pairs}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){combn}<LSEP>[](symbol){npops}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nlocpairpop}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pairs}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pop1}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){pops}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pop2}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){pops}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){pp1}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){pop1}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){pp2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){pop2}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){pp1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){pp2}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){index}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){mat_nloc_pops}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_nloc_pops}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){mat_nloc_pops}<LEND>[](symbol){nlocpairpop}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mat_nloc_pops}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){mat_nloc_pops}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){pops}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){pbar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){pb}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating zero_H/D_beta ......}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){zero_H_beta_es}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pairs}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pop1}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){pops}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pop2}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){pops}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){pp1}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){pop1}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){pp1}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){pp1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){pp1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.500000}<LSEP>[](symbol){pp1}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){pp2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){pop2}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){pp2}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){pp2}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){pp2}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.500000}<LSEP>[](symbol){pp2}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){pp1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){pp2}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){pp1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pp1}<LSEP>[](symbol){index}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){pp2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pp2}<LSEP>[](symbol){index}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){dummys}<LEND>[call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){pp1}<LSEP>[](symbol){pp2}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){dummys}<LEND>[argument 1; call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){dummys}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){dummys}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){dummys}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){zero_H_beta}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){zero_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){zero_H_beta_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){zero_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){zero_D_beta}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){zero_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){zero_D_beta_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){zero_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){mat_zero_H_beta}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_zero_H_beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){mat_zero_H_beta}<LEND>[](symbol){zero_H_beta}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_zero_H_beta}<LSEP>[](symbol){pairs}<LEND>[](symbol){zero_H_beta_sd}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mat_zero_H_beta}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){mat_zero_H_beta}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){pops}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){mat_zero_D_beta}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_zero_D_beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){mat_zero_D_beta}<LEND>[](symbol){zero_D_beta}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_zero_D_beta}<LSEP>[](symbol){pairs}<LEND>[](symbol){zero_D_beta_sd}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mat_zero_D_beta}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){mat_zero_D_beta}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){pops}<LEND>[statement 20; control flow](){if}<LSEP>[](symbol){pbar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){pb}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating one_H/D_beta ... }<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){gl}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){i0}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){p}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){logp}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.finite}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){p}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){log1_p}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.finite}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){one_H_alpha_all}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){logp}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){log1_p}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){one_H_beta_es}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pairs}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i1}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){pops}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i2}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){pops}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tt}<LEND>[call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){i0}<LSEP>[](symbol){i1}<LSEP>[](symbol){i2}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tt}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){tt}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){dummys}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){one_H_alpha_all}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){i0}<LSEP>[](symbol){index}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){one_H_alpha_es}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){dummys}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){i1}<LSEP>[](symbol){index}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){one_H_alpha_es}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){dummys}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){i2}<LSEP>[](symbol){index}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){dummys}<LEND>[argument 1; call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){dummys}<LEND>[argument 2; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){dummys}<LEND>[argument 3; call](){}<LSEP>[](symbol){sd}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){dummys}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){one_H_beta}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){one_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){one_H_beta_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){one_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){one_D_beta}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){one_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){one_D_beta_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){one_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){mat_one_H_beta}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 32; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_one_H_beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){mat_one_H_beta}<LEND>[](symbol){one_H_beta}<LEND>[statement 33; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_one_H_beta}<LSEP>[](symbol){pairs}<LEND>[](symbol){one_H_beta_sd}<LEND>[statement 34; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mat_one_H_beta}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){mat_one_H_beta}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){pops}<LEND>[statement 35; assign](){<-}<LSEP>[](symbol){mat_one_D_beta}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 36; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_one_D_beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){mat_one_D_beta}<LEND>[](symbol){one_D_beta}<LEND>[statement 37; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_one_D_beta}<LSEP>[](symbol){pairs}<LEND>[](symbol){one_D_beta_sd}<LEND>[statement 38; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mat_one_D_beta}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){mat_one_D_beta}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){pops}<LEND>[statement 39; control flow](){if}<LSEP>[](symbol){pbar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){pb}<LSEP>[argument 1; litteral](real){7.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating two_H/D_beta... }<LEND>[statement 40; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){gl}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 41; assign](){<-}<LSEP>[](symbol){i0}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){p}<LEND>[statement 42; assign](){<-}<LSEP>[](symbol){two_H_alpha_all}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 43; assign](){<-}<LSEP>[](symbol){two_H_beta_es}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){pairs}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i1}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){pops}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i2}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){pops}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tt}<LEND>[call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){i0}<LSEP>[](symbol){i1}<LSEP>[](symbol){i2}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tt}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){tt}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){m2Ha}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){two_H_alpha_es}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){dummys}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){i1}<LSEP>[](symbol){index}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){two_H_alpha_es}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){dummys}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){i2}<LSEP>[](symbol){index}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dummys}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){two_H_alpha_all}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){i0}<LSEP>[](symbol){index}<LEND>[](symbol){m2Ha}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){m2Ha}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){npops}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){npops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){dummys}<LEND>[argument 1; call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){dummys}<LEND>[argument 2; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){dummys}<LEND>[argument 3; call](){}<LSEP>[](symbol){sd}<LEND>[argument 0; call](){}<LSEP>[](symbol){exp}<LSEP>[](symbol){dummys}<LEND>[statement 44; assign](){<-}<LSEP>[](symbol){two_H_beta}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){two_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 45; assign](){<-}<LSEP>[](symbol){two_H_beta_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){two_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 46; assign](){<-}<LSEP>[](symbol){two_D_beta}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){two_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 47; assign](){<-}<LSEP>[](symbol){two_D_beta_sd}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){two_H_beta_es}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 48; assign](){<-}<LSEP>[](symbol){mat_two_H_beta}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 49; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_two_H_beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){mat_two_H_beta}<LEND>[](symbol){two_H_beta}<LEND>[statement 50; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_two_H_beta}<LSEP>[](symbol){pairs}<LEND>[](symbol){two_H_beta_sd}<LEND>[statement 51; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mat_two_H_beta}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){mat_two_H_beta}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){pops}<LEND>[statement 52; assign](){<-}<LSEP>[](symbol){mat_two_D_beta}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 53; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_two_D_beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){mat_two_D_beta}<LEND>[](symbol){two_D_beta}<LEND>[statement 54; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat_two_D_beta}<LSEP>[](symbol){pairs}<LEND>[](symbol){two_D_beta_sd}<LEND>[statement 55; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mat_two_D_beta}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){mat_two_D_beta}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){pops}<LEND>[statement 35; control flow](){if}<LSEP>[](symbol){pbar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){pb}<LSEP>[argument 1; litteral](real){8.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Done. ...}<LEND>[statement 36; control flow](){if}<LSEP>[](symbol){spectrumplot}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fs}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){zero_D_alpha}<LSEP>[](symbol){one_D_alpha}<LSEP>[](symbol){two_D_alpha}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cx}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){12.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){fs}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](real){0.025000}<LEND>[argument 1; litteral](real){0.500000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){bb}<LEND>[call](){}<LSEP>[](symbol){barplot}<LSEP>[](symbol){fs}<LSEP>[](symbol){T}<LEND>[argument 2; call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){fs}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.150000}<LEND>[argument 4; litteral](str){q-profile}<LEND>[argument 5; call](){}<LSEP>[](symbol){rainbow}<LSEP>[](symbol){npops}<LEND>[argument 6; litteral](real){2.000000}<LSEP>[argument 7; litteral](logical){FALSE}<LSEP>[](symbol){cx}<LEND>[statement 3; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LSEP>[](symbol){bb}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){2.100000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){q=0}<LSEP>[argument 1; litteral](str){q=1}<LSEP>[argument 2; litteral](str){q=2}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){sds}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){zero_D_alpha_sd}<LSEP>[](symbol){one_D_alpha_sd}<LSEP>[](symbol){two_D_alpha_sd}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){up}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){fs}<LSEP>[](symbol){sds}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){low}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){fs}<LSEP>[](symbol){sds}<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){confiplot}<LEND>[true branch; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){bb}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){ii}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){bb}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){arrows}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bb}<LSEP>[](symbol){ii}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){up}<LSEP>[](symbol){ii}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bb}<LSEP>[](symbol){ii}<LSEP>[](symbol){i}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){low}<LSEP>[](symbol){ii}<LSEP>[](symbol){i}<LEND>[argument 4; litteral](real){90.000000}<LSEP>[argument 5; litteral](real){3.000000}<LSEP>[argument 6; litteral](real){0.000000}<LEND>[statement 37; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){table}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){H}<LSEP>[argument 1; litteral](str){DH}<LSEP>[argument 2; litteral](str){HD}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tt}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){nlocpop}<LEND>[](symbol){zero_H_alpha}<LSEP>[](symbol){zero_H_alpha_sd}<LSEP>[](symbol){one_H_alpha}<LSEP>[](symbol){one_H_alpha_sd}<LSEP>[](symbol){two_H_alpha}<LSEP>[](symbol){two_H_alpha_sd}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){kable}<LEND>[](symbol){tt}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){npops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\npairwise non-missing loci}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){kable}<LEND>[](symbol){mat_nloc_pops}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\n0_H_beta}<LEND>[statement 3; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){kable}<LEND>[](symbol){mat_zero_H_beta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\n1_H_beta}<LEND>[statement 5; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){kable}<LEND>[](symbol){mat_one_H_beta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\n2_H_beta}<LEND>[statement 7; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){kable}<LEND>[](symbol){mat_two_H_beta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 38; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){table}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){D}<LSEP>[argument 1; litteral](str){DH}<LSEP>[argument 2; litteral](str){HD}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tt}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){nlocpop}<LEND>[](symbol){zero_D_alpha}<LSEP>[](symbol){zero_D_alpha_sd}<LSEP>[](symbol){one_D_alpha}<LSEP>[](symbol){one_D_alpha_sd}<LSEP>[](symbol){two_D_alpha}<LSEP>[](symbol){two_D_alpha_sd}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){kable}<LEND>[](symbol){tt}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){npops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\npairwise non-missing loci}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){kable}<LEND>[](symbol){mat_nloc_pops}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\n0_D_beta}<LEND>[statement 3; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){kable}<LEND>[](symbol){mat_zero_D_beta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\n1_D_beta}<LEND>[statement 5; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){kable}<LEND>[](symbol){mat_one_D_beta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\n2_D_beta}<LEND>[statement 7; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){kable}<LEND>[](symbol){mat_two_D_beta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 39; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){npops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){nlocpop}<LEND>[](symbol){mat_nloc_pops}<LSEP>[](symbol){zero_H_alpha}<LSEP>[](symbol){zero_H_alpha_sd}<LSEP>[](symbol){one_H_alpha}<LSEP>[](symbol){one_H_alpha_sd}<LSEP>[](symbol){two_H_alpha}<LSEP>[](symbol){two_H_alpha_sd}<LSEP>[](symbol){zero_D_alpha}<LSEP>[](symbol){zero_D_alpha_sd}<LSEP>[](symbol){one_D_alpha}<LSEP>[](symbol){one_D_alpha_sd}<LSEP>[](symbol){two_D_alpha}<LSEP>[](symbol){two_D_alpha_sd}<LSEP>[](symbol){mat_zero_H_beta}<LSEP>[](symbol){mat_one_H_beta}<LSEP>[](symbol){mat_two_H_beta}<LSEP>[](symbol){mat_zero_D_beta}<LSEP>[](symbol){mat_one_D_beta}<LSEP>[](symbol){mat_two_D_beta}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){nlocpop}<LEND>[](symbol){zero_H_alpha}<LSEP>[](symbol){zero_H_alpha_sd}<LSEP>[](symbol){one_H_alpha}<LSEP>[](symbol){one_H_alpha_sd}<LSEP>[](symbol){two_H_alpha}<LSEP>[](symbol){two_H_alpha_sd}<LSEP>[](symbol){zero_D_alpha}<LSEP>[](symbol){zero_D_alpha_sd}<LSEP>[](symbol){one_D_alpha}<LSEP>[](symbol){one_D_alpha_sd}<LSEP>[](symbol){two_D_alpha}<LSEP>[](symbol){two_D_alpha_sd}<LEND>[statement 40; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 41; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){out}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){cva}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gamma}<LEND>[call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){cov}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){y}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rrr_object}<LEND>[call](){}<LSEP>[](symbol){reduce_rank_regression}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){gamma}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){H}<LEND>[call](){}<LSEP>[](symbol){ginv}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){rrr_object}<LSEP>[argument 1; litteral](str){A}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){H}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){y}<LEND>[statement 4; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){rrr_object}<LSEP>[argument 1; litteral](str){mean}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){rrr_object}<LSEP>[argument 1; litteral](str){B}<LEND>[](symbol){H}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){rrr_object}<LSEP>[argument 1; litteral](str){eigen_values}<LEND>[assign](){<-}<LSEP>[](symbol){cva_scores}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cva_object}<LEND>[call](){}<LSEP>[](symbol){cva}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){correlation}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cva_object}<LSEP>[argument 1; litteral](str){canonical_corr}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){xi}<LEND>[call](){}<LSEP>[](symbol){as_data_frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cva_object}<LSEP>[argument 1; litteral](str){G}<LEND>[argument 1; call](){}<LSEP>[](symbol){organize}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){xi}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){xi}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){xi}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){omega}<LEND>[call](){}<LSEP>[](symbol){as_data_frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cva_object}<LSEP>[argument 1; litteral](str){H}<LEND>[argument 1; call](){}<LSEP>[](symbol){organize}<LSEP>[](symbol){y}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){omega}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){omega}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){omega}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){}<LEND>[statement 6; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){xi}<LSEP>[](symbol){omega}<LSEP>[](symbol){correlation}<LEND>[assign](){<-}<LSEP>[](symbol){cva_error}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){x_new}<LSEP>[](symbol){y_new}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cva_object}<LEND>[call](){}<LSEP>[](symbol){cva}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){data_frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){y_new}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){error}<LEND>[call](){}<LSEP>[](symbol){as_data_frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cva_object}<LSEP>[argument 1; litteral](str){H}<LEND>[argument 1; call](){}<LSEP>[](symbol){organize}<LSEP>[](symbol){y_new}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cva_object}<LSEP>[argument 1; litteral](str){G}<LEND>[argument 1; call](){}<LSEP>[](symbol){organize}<LSEP>[](symbol){x_new}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){error}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){CV}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){error}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){bind_cols}<LEND>[](symbol){index}<LSEP>[](symbol){error}<LEND>[assign](){<-}<LSEP>[](symbol){cva_residual}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cva_error}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LEND>[assign](){<-}<LSEP>[](symbol){cva_residual_plot}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){residuals}<LEND>[call](){}<LSEP>[](symbol){cva_residual}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){static_plot}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){GGally}<LSEP>[](symbol){ggpairs}<LEND>[](symbol){residuals}<LEND>[argument 1; call](){}<LSEP>[](symbol){labs}<LSEP>[argument 0; litteral](str){CVA Residuals}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){static_plot}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){ggplot}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){plot}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[](symbol){residuals}<LEND>[false branch; block](){}<LSEP>[](symbol){static_plot}<LEND>[assign](){<-}<LSEP>[](symbol){cva_rank_trace}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){k}<LSEP>[](symbol){plot}<LSEP>[](symbol){interactive}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gamma}<LEND>[call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){cov}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){y}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){plot}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){interactive}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rt}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){rrr_rank_trace}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){gamma}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){ggtitle}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){CVA Rank Trace Plot, k = }<LSEP>[](symbol){k}<LSEP>[argument 2; litteral](str){}<LEND>[statement 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){plotly}<LSEP>[](symbol){ggplotly}<LEND>[](symbol){rt}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){plot}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){interactive}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){rrr_rank_trace}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){gamma}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){ggtitle}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){CVA Rank Trace Plot, k = }<LSEP>[](symbol){k}<LSEP>[argument 2; litteral](str){}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){rrr_rank_trace}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){gamma}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[assign](){<-}<LSEP>[](symbol){cva_residual_3D_plot}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){cva_x}<LSEP>[](symbol){cva_y}<LSEP>[](symbol){cva_z}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LSEP>[](symbol){point_size}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){residuals}<LEND>[call](){}<LSEP>[](symbol){cva_residual}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){rank}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){resids}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){residuals}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){residuals}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){resid_x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){resids}<LSEP>[](symbol){}<LSEP>[](symbol){cva_x}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){resid_y}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){resids}<LSEP>[](symbol){}<LSEP>[](symbol){cva_y}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){resid_z}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){resids}<LSEP>[](symbol){}<LSEP>[](symbol){cva_z}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){resid_tbl}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){dplyr}<LSEP>[](symbol){bind_cols}<LEND>[](symbol){resid_x}<LSEP>[](symbol){resid_y}<LSEP>[](symbol){resid_z}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){resid_tbl}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){resid_x}<LSEP>[argument 1; litteral](str){resid_y}<LSEP>[argument 2; litteral](str){resid_z}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){ptsize}<LSEP>[](symbol){point_size}<LEND>[statement 8; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){plotly}<LSEP>[](symbol){plot_ly}<LEND>[](symbol){resid_tbl}<LEND>[argument 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){resid_x}<LEND>[argument 2; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){resid_y}<LEND>[argument 3; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){resid_z}<LEND>[argument 4; litteral](str){scatter3d}<LSEP>[argument 5; litteral](str){marker}<LEND>[argument 6; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){ptsize}<LEND>[argument 7; litteral](str){CVA 3D Residual Scatter Plot}<LEND>[assign](){<-}<LSEP>[](symbol){cva_pairwise_plot}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){cv_pair}<LSEP>[](symbol){k}<LSEP>[](symbol){interactive}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){scores_object}<LEND>[call](){}<LSEP>[](symbol){cva_scores}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){cv_pair}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){corr}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){scores_object}<LSEP>[argument 1; litteral](str){canonical_corr}<LEND>[](symbol){cv_pair}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){x_axis}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){scores_object}<LSEP>[argument 1; litteral](str){xi}<LEND>[](symbol){}<LSEP>[](symbol){cv_pair}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){y_axis}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){scores_object}<LSEP>[argument 1; litteral](str){omega}<LEND>[](symbol){}<LSEP>[](symbol){cv_pair}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){bind_cols}<LSEP>[](symbol){x_axis}<LSEP>[](symbol){y_axis}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){static_plot}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ggplot}<LSEP>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes_q}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.name}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){df}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.name}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){df}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_point}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_smooth}<LSEP>[argument 0; litteral](str){lm}<LEND>[argument 1; call](){}<LSEP>[](symbol){labs}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){CV}<LSEP>[](symbol){cv_pair}<LSEP>[argument 2; litteral](str){ Pairwise Plot, Canonical Corr...}<LEND>[argument 3; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){corr}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 4; litteral](str){}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){interactive}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){plotly}<LSEP>[](symbol){ggplotly}<LEND>[](symbol){static_plot}<LEND>[false branch; block](){}<LSEP>[](symbol){static_plot}

[](){expression}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.test.heterozygosity}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){nreps}<LSEP>[](symbol){alpha1}<LSEP>[](symbol){alpha2}<LSEP>[](symbol){plot}<LSEP>[](symbol){plot.out}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){alpha1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){alpha1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: First alpha value sho...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){alpha1}<LSEP>[litteral](real){0.050000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){alpha2}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){alpha1}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Second alpha value sh...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){alpha1}<LSEP>[litteral](real){0.010000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){upper1}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){alpha1}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){upper2}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){alpha2}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){upper1}<LSEP>[](symbol){upper2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tmp}<LSEP>[](symbol){upper2}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){upper2}<LSEP>[](symbol){upper1}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){upper1}<LSEP>[](symbol){tmp}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){lower1}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){upper1}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){lower2}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){upper2}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: genlight object con...}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){gl.report.heterozygosity}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){D}<LEND>[call](){}<LSEP>[](symbol){outer}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){out}<LSEP>[](symbol){He}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){out}<LSEP>[](symbol){He}<LEND>[argument 2; litteral](str){-}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating the sampling dis...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Please be patient .... go ha...}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[](symbol){nreps}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 20; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nreps}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[](symbol){n}<LSEP>[](symbol){T}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){gl.report.heterozygosity}<LSEP>[](symbol){x2}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){outer}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){out}<LSEP>[](symbol){He}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){out}<LSEP>[](symbol){He}<LEND>[argument 2; litteral](str){-}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){pop1}<LSEP>[argument 1; litteral](str){pop2}<LSEP>[argument 2; litteral](str){diff}<LSEP>[argument 3; litteral](str){significance}<LSEP>[argument 4; litteral](str){pval}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){count}<LSEP>[litteral](real){0.000000}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Cycling through the}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){pairs of populations\n}<LEND>[statement 25; control flow](){for}<LSEP>[](symbol){first}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){second}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){first}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){obs}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){D}<LSEP>[](symbol){first}<LSEP>[](symbol){second}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){u1quantile}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){quantile}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){first}<LSEP>[](symbol){second}<LSEP>[](symbol){}<LEND>[](symbol){upper1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){u2quantile}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){quantile}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){first}<LSEP>[](symbol){second}<LSEP>[](symbol){}<LEND>[](symbol){upper2}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){l1quantile}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){quantile}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){first}<LSEP>[](symbol){second}<LSEP>[](symbol){}<LEND>[](symbol){lower1}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){l2quantile}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){quantile}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){first}<LSEP>[](symbol){second}<LSEP>[](symbol){}<LEND>[](symbol){lower2}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){u2quantile}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){l2quantile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){signif}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){non-sig @}<LSEP>[](symbol){lower2}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){u1quantile}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){l1quantile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){signif}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){non-sig @}<LSEP>[](symbol){lower1}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){u1quantile}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){l1quantile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){signif}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){sig @}<LSEP>[](symbol){lower1}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){u2quantile}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){l2quantile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){signif}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){sig @}<LSEP>[](symbol){lower2}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){values}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){first}<LSEP>[](symbol){second}<LSEP>[](symbol){}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){values}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){values}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){values}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){values}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){values}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){pop1}<LEND>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[](symbol){first}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){pop2}<LEND>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[](symbol){second}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){diff}<LEND>[](symbol){count}<LEND>[](symbol){obs}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){significance}<LEND>[](symbol){count}<LEND>[](symbol){signif}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){pval}<LEND>[](symbol){count}<LEND>[](symbol){p}<LEND>[statement 18; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Plotting sampling distributi...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){label}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[](symbol){first}<LEND>[argument 1; litteral](str){ x }<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[](symbol){second}<LEND>[argument 3; litteral](str){ -- }<LSEP>[](symbol){signif}<LSEP>[argument 5; litteral](str){ (p = }<LSEP>[](symbol){p}<LSEP>[argument 7; litteral](str){)}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){values}<LSEP>[argument 1; litteral](real){100.000000}<LSEP>[](symbol){label}<LSEP>[argument 3; litteral](str){difference}<LSEP>[](symbol){F}<LSEP>[argument 5; litteral](str){gray}<LEND>[statement 3; call](){}<LSEP>[](symbol){abline}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](str){blue}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){abline}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){D}<LSEP>[](symbol){first}<LSEP>[](symbol){second}<LEND>[argument 1; litteral](str){green}<LEND>[statement 5; call](){}<LSEP>[](symbol){abline}<LSEP>[](symbol){u1quantile}<LSEP>[argument 1; litteral](str){red}<LEND>[statement 6; call](){}<LSEP>[](symbol){abline}<LSEP>[](symbol){u2quantile}<LSEP>[argument 1; litteral](str){red}<LEND>[statement 7; call](){}<LSEP>[](symbol){abline}<LSEP>[](symbol){l1quantile}<LSEP>[argument 1; litteral](str){red}<LEND>[statement 8; call](){}<LSEP>[](symbol){abline}<LSEP>[](symbol){l2quantile}<LSEP>[argument 1; litteral](str){red}<LEND>[statement 9; call](){}<LSEP>[](symbol){text}<LSEP>[](symbol){u1quantile}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){density}<LEND>[](symbol){upper1}<LSEP>[argument 3; litteral](str){blue}<LSEP>[argument 4; litteral](real){0.600000}<LSEP>[argument 5; litteral](real){0.000000}<LEND>[statement 10; call](){}<LSEP>[](symbol){text}<LSEP>[](symbol){u2quantile}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){density}<LEND>[](symbol){upper2}<LSEP>[argument 3; litteral](str){blue}<LSEP>[argument 4; litteral](real){0.600000}<LSEP>[argument 5; litteral](real){0.000000}<LEND>[statement 11; call](){}<LSEP>[](symbol){text}<LSEP>[](symbol){l1quantile}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){density}<LEND>[](symbol){lower1}<LSEP>[argument 3; litteral](str){blue}<LSEP>[argument 4; litteral](real){0.600000}<LSEP>[argument 5; litteral](real){1.000000}<LEND>[statement 12; call](){}<LSEP>[](symbol){text}<LSEP>[](symbol){l2quantile}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){density}<LEND>[](symbol){lower2}<LSEP>[argument 3; litteral](str){blue}<LSEP>[argument 4; litteral](real){0.600000}<LSEP>[argument 5; litteral](real){1.000000}<LEND>[statement 13; call](){}<LSEP>[](symbol){text}<LSEP>[](symbol){obs}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){density}<LEND>[argument 2; litteral](str){OBS}<LSEP>[argument 3; litteral](str){blue}<LSEP>[argument 4; litteral](real){0.600000}<LSEP>[argument 5; litteral](real){0.500000}<LEND>[statement 14; call](){}<LSEP>[](symbol){text}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){density}<LEND>[argument 2; litteral](str){0}<LSEP>[argument 3; litteral](str){blue}<LSEP>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){1.000000}<LEND>[statement 19; control flow](){if}<LSEP>[](symbol){plot.out}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Outputting plots as jpeg fil...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){plot.name}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[](symbol){first}<LEND>[argument 1; litteral](str){ x }<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[](symbol){second}<LEND>[argument 3; litteral](str){.jpg}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){dev.copy}<LEND>[argument 0; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){jpeg}<LEND>[](symbol){plot.name}<LEND>[statement 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){dev.off}<LEND>[statement 26; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 27; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){df}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){as.foldert.array}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){ind}<LSEP>[](symbol){var}<LSEP>[](symbol){time}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){name.x}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){name.g}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){timecol}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.array}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){name.x}<LSEP>[argument 1; litteral](str){is not an array.}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){3.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){name.x}<LSEP>[argument 1; litteral](str){: wrong number of dimensions.}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){ind}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){var}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){time}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){aperm}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){ind}<LSEP>[](symbol){var}<LSEP>[](symbol){time}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){ntimes}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){times}<LEND>[call](){}<LSEP>[](symbol){as.ordered}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){times}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){times}<LEND>[call](){}<LSEP>[](symbol){as.ordered}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntimes}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){fold}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 9; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntimes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xk}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){}<LSEP>[](symbol){k}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fold}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){xk}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fold}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){xk}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fold}<LEND>[](symbol){times}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){foldt}<LEND>[call](){}<LSEP>[](symbol){foldert}<LSEP>[](symbol){fold}<LSEP>[](symbol){times}<LSEP>[argument 2; litteral](str){union}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){foldt}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){is.fpcad}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){fpcad}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){getrow.foldert}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){name}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.foldert}<LSEP>[](symbol){object}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){getrow.foldert applies to an o...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){objk}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){object}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xf}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){objk}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){objk}<LEND>[](symbol){name}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){object}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){xf}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.set.verbosity}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){value}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: genlight object...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence ...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Setting default verbosity to}<LSEP>[](symbol){value}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[](symbol){value}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){checkIndex}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){findex}<LSEP>[](symbol){mindex}<LSEP>[](symbol){gindex}<LSEP>[](symbol){excludefp}<LSEP>[](symbol){fast}<LSEP>[](symbol){warn}<LSEP>[](symbol){logfile}<LSEP>[](symbol){quiet}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){alldupli}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){\ncheckIndex results at }<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[argument 2; litteral](str){ for\n}<LSEP>[](symbol){dwdbase}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){itime}<LEND>[call](){}<LSEP>[](symbol){file.mtime}<LSEP>[argument 0; litteral](str){data/fileIndex.rda}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){itime}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){\nFile 'data/fileIndex.rda' wa...}<LSEP>[](symbol){itime}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){traceCall}<LEND>[argument 0; litteral](real){1.000000}<LEND>[argument 2; litteral](str){-------}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){findex}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Checking fileIndex...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){duplifile}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){findex}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){minute}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){res}<LEND>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){duplifile}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){duplifile}<LEND>[argument 1; call](){}<LSEP>[](symbol){alldupli}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){duplifile}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){duplifile}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){id}<LEND>[](symbol){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){duplifile}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){duplifile}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){res}<LEND>[argument 1; litteral](str){subdaily}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){var}<LEND>[argument 1; litteral](str){standard_format}<LEND>[](symbol){}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){duplifile}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rvp}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){var}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){per}<LEND>[argument 3; litteral](str){/}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){per_folder}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){rvp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){id}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rvp}<LSEP>[](symbol){p}<LEND>[statement 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){- }<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){round0}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](str){ }<LEND>[argument 2; litteral](str){ at }<LSEP>[](symbol){p}<LSEP>[argument 4; litteral](str){; }<LEND>[argument 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){truncMessage}<LEND>[](symbol){i}<LSEP>[argument 1; litteral](real){10.000000}<LSEP>[argument 2; litteral](str){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){per_folder}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){per_folder}<LEND>[argument 1; litteral](str){\n}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){IDs with duplicate files:}<LSEP>[](symbol){per_folder}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){duplifile}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){findex}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){ismeta}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){txt$}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){path}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){res}<LEND>[argument 1; litteral](str){multi_annual}<LEND>[](symbol){}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){rvp}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){var}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){per}<LEND>[argument 3; litteral](str){/}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){duplifile}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){path}<LEND>[argument 1; call](){}<LSEP>[](symbol){alldupli}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){duplifile}<LSEP>[](symbol){rvp}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){duplifile}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){Duplicate 'Beschreibung' files:}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){-}<LSEP>[](symbol){duplifile}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){mindex}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Checking metaIndex...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newout}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){out}<LSEP>[](symbol){ids}<LSEP>[](symbol){colcomp}<LSEP>[](symbol){column}<LSEP>[](symbol){textvar}<LSEP>[](symbol){unit}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){new}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){ids}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tt}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mindex}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){colcomp}<LSEP>[](symbol){i}<LEND>[](symbol){column}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; call](){}<LSEP>[](symbol){unname}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){- }<LSEP>[](symbol){textvar}<LSEP>[argument 2; litteral](str){=}<LSEP>[](symbol){i}<LSEP>[argument 4; litteral](str){: }<LEND>[argument 5; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){tt}<LSEP>[argument 1; litteral](str){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tt}<LEND>[](symbol){unit}<LSEP>[argument 4; litteral](str){, }<LEND>[statement 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){out}<LSEP>[](symbol){new}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){id_uni}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){Stations_id}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){eletol}<LSEP>[litteral](real){2.100000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){id_ele}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){pbapply}<LSEP>[](symbol){pbsapply}<LEND>[](symbol){id_uni}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){diff}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mindex}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){Stations_id}<LEND>[](symbol){i}<LEND>[argument 2; litteral](str){Stationshoehe}<LEND>[](symbol){eletol}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){id_ele}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Elevation differences >}<LSEP>[](symbol){eletol}<LSEP>[argument 2; litteral](str){m:}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){newout}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id_uni}<LSEP>[](symbol){id_ele}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){Stations_id}<LEND>[argument 3; litteral](str){Stationshoehe}<LSEP>[argument 4; litteral](str){ID}<LSEP>[argument 5; litteral](str){m}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){fast}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){loctol}<LSEP>[litteral](real){0.040000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){id_loc}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){pbapply}<LSEP>[](symbol){pbsapply}<LEND>[](symbol){id_uni}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){maxlldist}<LSEP>[argument 0; litteral](str){geoBreite}<LSEP>[argument 1; litteral](str){geoLaenge}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mindex}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){Stations_id}<LEND>[](symbol){i}<LEND>[](symbol){}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[](symbol){loctol}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){coord}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){geoBreite}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){geoLaenge}<LEND>[argument 2; litteral](str){_}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){id_loc}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Location differences >}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){loctol}<LSEP>[argument 1; litteral](real){1000.000000}<LEND>[argument 2; litteral](str){m:}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){newout}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id_uni}<LSEP>[](symbol){id_loc}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){Stations_id}<LEND>[argument 3; litteral](str){coord}<LSEP>[argument 4; litteral](str){ID}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){id_name}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){pbapply}<LSEP>[](symbol){pbsapply}<LEND>[](symbol){id_uni}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mindex}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){Stations_id}<LEND>[](symbol){i}<LEND>[argument 2; litteral](str){Stationsname}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){id_name}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){Different names per id:}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){newout}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id_uni}<LSEP>[](symbol){id_name}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){Stations_id}<LEND>[argument 3; litteral](str){Stationsname}<LSEP>[argument 4; litteral](str){ID}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){name_uni}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){Stationsname}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){name_id}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){pbapply}<LSEP>[](symbol){pbsapply}<LEND>[](symbol){name_uni}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){n}<LEND>[body; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mindex}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){Stationsname}<LEND>[](symbol){n}<LEND>[argument 2; litteral](str){Stations_id}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 11; control flow](){if}<LSEP>[](symbol){excludefp}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){name_id}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){name_uni}<LSEP>[argument 1; litteral](str){Suderburg}<LEND>[litteral](logical){FALSE}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){name_id}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){More than one id per name:}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){newout}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){name_uni}<LSEP>[](symbol){name_id}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){Stationsname}<LEND>[argument 3; litteral](str){Stations_id}<LSEP>[argument 4; litteral](str){Name}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){findex}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){mindex}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Comparing fileIndex and metaIn...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){start}<LEND>[call](){}<LSEP>[](symbol){as.Date}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){start}<LEND>[argument 1; litteral](str){%Y%m%d}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){end}<LEND>[call](){}<LSEP>[](symbol){as.Date}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){end}<LEND>[argument 1; litteral](str){%Y%m%d}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){von_datum}<LEND>[call](){}<LSEP>[](symbol){as.Date}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){von_datum}<LEND>[argument 1; litteral](str){%Y%m%d}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){bis_datum}<LEND>[call](){}<LSEP>[](symbol){as.Date}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){bis_datum}<LEND>[argument 1; litteral](str){%Y%m%d}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){m2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mindex}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){res}<LEND>[argument 1; litteral](str){annual}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){var}<LEND>[argument 1; litteral](str){more_precip}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){per}<LEND>[argument 1; litteral](str){historical}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mindex}<LSEP>[](symbol){hasfile}<LEND>[](symbol){}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){f2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){findex}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){res}<LEND>[argument 1; litteral](str){annual}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){var}<LEND>[argument 1; litteral](str){more_precip}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){per}<LEND>[argument 1; litteral](str){historical}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){id}<LEND>[](symbol){}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){mf}<LEND>[call](){}<LSEP>[](symbol){merge}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m2}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Stations_id}<LSEP>[argument 1; litteral](str){von_datum}<LSEP>[argument 2; litteral](str){bis_datum}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){f2}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){id}<LSEP>[argument 1; litteral](str){start}<LSEP>[argument 2; litteral](str){end}<LEND>[argument 2; litteral](str){Stations_id}<LSEP>[argument 3; litteral](str){id}<LEND>[statement 8; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){m2}<LSEP>[](symbol){f2}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mf}<LSEP>[](symbol){diff_von}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.integer}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mf}<LSEP>[](symbol){start}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mf}<LSEP>[](symbol){von_datum}<LEND>[argument 1; litteral](real){365.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mf}<LSEP>[](symbol){diff_bis}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.integer}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mf}<LSEP>[](symbol){end}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mf}<LSEP>[](symbol){bis_datum}<LEND>[argument 1; litteral](real){365.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mf}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){_datum}<LSEP>[argument 1; litteral](str){_meta}<LEND>[argument 2; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mf}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mf}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){start}<LSEP>[argument 1; litteral](str){von_file}<LEND>[argument 2; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mf}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mf}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){end}<LSEP>[argument 1; litteral](str){bis_file}<LEND>[argument 2; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mf}<LEND>[statement 14; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mf}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mf}<LSEP>[](symbol){diff_von}<LEND>[argument 1; litteral](real){5.000000}<LEND>[](symbol){}<LEND>[statement 15; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mf}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){mf}<LSEP>[](symbol){diff_bis}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){30.000000}<LEND>[](symbol){}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){gindex}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Checking geoIndex...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){columns}<LEND>[call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){gindex}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){display}<LSEP>[argument 1; litteral](str){col}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){fpid}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){14306.000000}<LSEP>[argument 1; litteral](real){921.000000}<LSEP>[argument 2; litteral](real){13967.000000}<LSEP>[argument 3; litteral](real){13918.000000}<LSEP>[argument 4; litteral](real){14317.000000}<LSEP>[argument 5; litteral](real){3024.000000}<LSEP>[argument 6; litteral](real){2158.000000}<LSEP>[argument 7; litteral](real){7434.000000}<LSEP>[argument 8; litteral](real){785.000000}<LSEP>[argument 9; litteral](real){787.000000}<LSEP>[argument 10; litteral](real){15526.000000}<LSEP>[argument 11; litteral](real){5248.000000}<LSEP>[argument 12; litteral](real){5249.000000}<LSEP>[argument 13; litteral](real){396.000000}<LSEP>[argument 14; litteral](real){397.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){gindex_id}<LSEP>[](symbol){gindex}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){excludefp}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){gindex_id}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gindex}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gindex}<LSEP>[](symbol){id}<LEND>[](symbol){fpid}<LEND>[](symbol){}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){coord}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gindex_id}<LSEP>[](symbol){lon}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gindex_id}<LSEP>[](symbol){lat}<LEND>[argument 2; litteral](str){_}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){anyDuplicated}<LSEP>[](symbol){coord}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){Coordinates used for more than...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){new}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){coord}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){coord}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){c}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gindex_id}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){coord}<LSEP>[](symbol){c}<LEND>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){toString}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){g}<LSEP>[](symbol){nfiles}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){g}<LSEP>[](symbol){nonpublic}<LEND>[argument 1; litteral](str){x ID=}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){g}<LSEP>[](symbol){id}<LEND>[argument 3; litteral](str){ (}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){g}<LSEP>[](symbol){name}<LEND>[argument 5; litteral](str){)}<LEND>[statement 2; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){- }<LSEP>[](symbol){c}<LSEP>[argument 2; litteral](str){: }<LSEP>[](symbol){t}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){out}<LSEP>[](symbol){new}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){logfileprint}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){logfile}<LEND>[true branch; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){ openFile('}<LEND>[argument 1; call](){}<LSEP>[](symbol){normalizePath}<LSEP>[](symbol){logfile}<LSEP>[argument 1; litteral](str){/}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[argument 2; litteral](str){')}<LEND>[false branch; litteral](str){}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){out}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){warn}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){There are issues in the indexes.}<LSEP>[](symbol){logfileprint}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){\n}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){\n}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){logfile}<LEND>[true branch; call](){}<LSEP>[](symbol){cat}<LSEP>[](symbol){out}<LSEP>[](symbol){logfile}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 14; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){out}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){FL}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){...}<LSEP>[](symbol){.n}<LSEP>[](symbol){pattern}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){new}<LSEP>[argument 0; litteral](str){FormulaList}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[](symbol){.n}<LSEP>[](symbol){pattern}<LEND>[call](){}<LSEP>[](symbol){%type%}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){list}<LEND>[argument 1; call](){}<LSEP>[](symbol){FormulaList}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){.n}<LSEP>[](symbol){ANY}<LEND>[argument 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){pattern}<LSEP>[](symbol){character}<LEND>[](symbol){.Object}<LEND>[call](){}<LSEP>[](symbol){setAs}<LSEP>[argument 0; litteral](str){list}<LSEP>[argument 1; litteral](str){FormulaList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){from}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){new}<LSEP>[argument 0; litteral](str){FormulaList}<LSEP>[](symbol){from}<LSEP>[argument 2; litteral](NULL){NULL}<LSEP>[argument 3; litteral](str){\\.n}<LEND>[assign](){<-}<LSEP>[](symbol){makeFormulas}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){...}<LSEP>[](symbol){.n}<LSEP>[](symbol){pattern}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){formulas}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[statement 1; call](){}<LSEP>[](symbol){map}<LSEP>[](symbol){formulas}<LEND>[argument 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){f}<LEND>[argument 1; call](){}<LSEP>[](symbol){stopifnot}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){formula}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){.each}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){.n}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){.n}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){.n}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){formulas}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){formulaList}<LEND>[call](){}<LSEP>[](symbol){map}<LSEP>[](symbol){formulas}<LSEP>[](symbol){deparse}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){formulaList}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){formulaList}<LSEP>[](symbol){.each}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){formulaList}<LEND>[call](){}<LSEP>[](symbol){map}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){pattern}<LSEP>[](symbol){.n}<LEND>[](symbol){formulaList}<LEND>[](symbol){gsub}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){formulaList}<LEND>[call](){}<LSEP>[](symbol){map}<LSEP>[](symbol){formulaList}<LSEP>[](symbol){as.formula}<LEND>[argument 2; call](){}<LSEP>[](symbol){environment}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){formulas}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){formulaList}<LEND>[call](){}<LSEP>[](symbol){map}<LSEP>[](symbol){formulaList}<LSEP>[](symbol){TwoSidedFormula}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){formulaList}<LEND>[litteral](NULL){NULL}<LEND>[](symbol){formulaList}<LEND>[assign](){<-}<LSEP>[](symbol){update.NULL}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; litteral](NULL){NULL}<LEND>[assign](){<-}<LSEP>[](symbol){update.FormulaList}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){data}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){object}<LSEP>[](symbol){.n}<LEND>[true branch; block](){}<LSEP>[](symbol){object}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.list}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){object}<LSEP>[](symbol){.n}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){new}<LSEP>[argument 0; litteral](str){FormulaList}<LSEP>[argument 1; litteral](NULL){NULL}<LEND>[argument 2; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){object}<LSEP>[](symbol){pattern}<LEND>[argument 3; call](){}<LSEP>[](symbol){substituteFormulas}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){object}<LSEP>[](symbol){.n}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){.n}<LEND>[call](){}<LSEP>[](symbol){extractNames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){object}<LSEP>[](symbol){.n}<LEND>[statement 1; call](){}<LSEP>[](symbol){new}<LSEP>[argument 0; litteral](str){FormulaList}<LEND>[argument 1; call](){}<LSEP>[](symbol){do.call}<LSEP>[](symbol){makeFormulas}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){.n}<LEND>[argument 1; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){object}<LSEP>[](symbol){pattern}<LEND>[assign](){<-}<LSEP>[](symbol){extractNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){ind}<LSEP>[](symbol){...}<LEND>[body; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){extract}<LSEP>[](symbol){x}<LSEP>[](symbol){ind}<LEND>[assign](){<-}<LSEP>[](symbol){substituteFormulas}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){listOfFormulas}<LSEP>[](symbol){.n}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){listOfFormulas}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){f}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){env}<LEND>[call](){}<LSEP>[](symbol){environment}<LSEP>[](symbol){f}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){subs}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){.n}<LSEP>[](symbol){asQuoted}<LEND>[statement 2; call](){}<LSEP>[](symbol){formula}<LEND>[argument 0; call](){}<LSEP>[](symbol){eval}<LEND>[argument 0; call](){}<LSEP>[](symbol){call}<LSEP>[argument 0; litteral](str){substitute}<LSEP>[](symbol){f}<LSEP>[](symbol){subs}<LEND>[](symbol){env}<LEND>[assign](){<-}<LSEP>[](symbol){asQuoted}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.formula}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){~}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.save}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){file}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Saving Presence/Absence (Sil...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Saving a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Saving an object of Class:}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){other}<LEND>[statement 6; call](){}<LSEP>[](symbol){saveRDS}<LSEP>[](symbol){x}<LSEP>[](symbol){file}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](real){2.000000}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.make.recode.ind}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){out.recode.file}<LSEP>[](symbol){outpath}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){outfilespec}<LEND>[call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){outpath}<LSEP>[](symbol){out.recode.file}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Creating draft lookup table\n}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Writing draft lookup table to}<LSEP>[](symbol){outfilespec}<LSEP>[argument 2; litteral](str){. Edit before use\n}<LEND>[statement 11; call](){}<LSEP>[](symbol){write.table}<LSEP>[](symbol){mat}<LSEP>[](symbol){outfilespec}<LSEP>[argument 2; litteral](str){,}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 13; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){fn}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){fn}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){gradient_hessian}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){gradient_hessian}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){rss}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){rss}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){rss_fixed}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){known_param}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){rss_fixed}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){rss_gradient_hessian}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){rss_gradient_hessian}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){rss_gradient_hessian_fixed}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){known_param}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){rss_gradient_hessian_fixed}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){mle_asy}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){mle_asy}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){init}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){init}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){fit}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){fit}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){fit_constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){fit_constrained}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){fisher_info}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){theta}<LSEP>[](symbol){sigma}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){fisher_info}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){curve_variance}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){curve_variance}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){nauc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){xlim}<LSEP>[](symbol){ylim}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){nauc}<LSEP>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){naac}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){xlim}<LSEP>[](symbol){ylim}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){naac}<LSEP>[](symbol){object}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){sqrtmatrix}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){mat}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){isSymmetric}<LSEP>[](symbol){mat}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The matrix must be symmetric}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ep}<LEND>[call](){}<LSEP>[](symbol){eigen}<LSEP>[](symbol){mat}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){i.neg}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ep}<LSEP>[](symbol){values}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){i.neg}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){All eigenvalues of the matrix ...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){i.small}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ep}<LSEP>[](symbol){values}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){i.small}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ep}<LSEP>[](symbol){values}<LEND>[](symbol){i.small}<LEND>[litteral](real){0.000000}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){valp}<LEND>[call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ep}<LSEP>[](symbol){values}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){vecp}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ep}<LSEP>[](symbol){vectors}<LEND>[statement 8; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){vecp}<LSEP>[](symbol){valp}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){vecp}

[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){varplot}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){plot.it}<LSEP>[](symbol){type}<LSEP>[](symbol){max.var.show}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ada}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Object must be of type 'ada'}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){type}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){type}<LSEP>[litteral](str){none}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){iter}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){iter}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nm}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){names}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){vec}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nm}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){dim}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){g1}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LSEP>[](symbol){obj}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){obj}<LSEP>[](symbol){i}<LEND>[](symbol){frame}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){p}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){imp}<LEND>[call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){obj}<LSEP>[](symbol){i}<LEND>[](symbol){splits}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vals}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){obj}<LSEP>[](symbol){i}<LEND>[](symbol){splits}<LEND>[](symbol){nm}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){vec}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){p}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vec}<LSEP>[](symbol){vals}<LEND>[](symbol){imp}<LEND>[](symbol){vec}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){vec}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){iter}<LEND>[argument 1; call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){iter}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; call](){}<LSEP>[](symbol){g1}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){model}<LEND>[](symbol){trees}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){sum}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){vars}<LEND>[call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){vec}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){vec}<LEND>[statement 10; assign](){=}<LSEP>[](symbol){max.v}<LSEP>[](symbol){max.var.show}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){p}<LSEP>[](symbol){max.v}<LEND>[true branch; assign](){=}<LSEP>[](symbol){max.v}<LSEP>[](symbol){p}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){plot.it}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){dotchart}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vec}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vars}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){max.v}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nm}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vars}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){max.v}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){Score}<LSEP>[argument 3; litteral](str){Variable Importance Plot}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){scores}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){vars}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vars}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){max.v}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){t1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vec}<LSEP>[](symbol){vars}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){t1}<LSEP>[argument 1; litteral](str){names}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nm}<LSEP>[](symbol){vars}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){t1}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rmcol.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){name}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){object}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){rmcol.folder applies to an obj...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){object}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[](symbol){name}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){object}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){xf}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.filter.parent.offspring}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){min.rdepth}<LSEP>[](symbol){min.reproducibility}<LSEP>[](symbol){range}<LSEP>[](symbol){rm.monomorphs}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Detected Presence...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){hold}<LSEP>[](symbol){x}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Generating null expectation ...}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.reassign.pop}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){id}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.filter.reproducibility}<LSEP>[](symbol){x}<LSEP>[](symbol){min.reproducibility}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.filter.rdepth}<LSEP>[](symbol){x}<LSEP>[](symbol){min.rdepth}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.filter.callrate}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.950000}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[argument 3; litteral](real){0.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){nL}<LEND>[call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){nP}<LEND>[call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){pN}<LEND>[call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){nP}<LSEP>[](symbol){nP}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[statement 19; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){nP}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){nP}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pair}<LEND>[call](){}<LSEP>[](symbol){gl.keep.pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pN}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pN}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){pair}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vect}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){homalts}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){vect}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){vect}<LSEP>[argument 1; litteral](real){20.000000}<LEND>[](symbol){T}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){count}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[](symbol){homalts}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){counts}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){count}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){count}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Identifying outliers with lo...}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){title}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){SNP data (DArTSeq)\nCounts of ...}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){op}<LEND>[call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[argument 1; litteral](real){0.500000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[argument 3; litteral](str){m}<LEND>[statement 24; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.500000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Standard boxplot, no adjustm...}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){whisker}<LEND>[call](){}<LSEP>[](symbol){boxplot}<LSEP>[](symbol){counts}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){steelblue}<LSEP>[](symbol){range}<LSEP>[](symbol){title}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){lower.extremes}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){median}<LSEP>[](symbol){counts}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lower.extremes}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outliers}<LSEP>[litteral](NULL){NULL}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outliers}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){lower.extremes}<LEND>[statement 29; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Identifying outlying pairs\n}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){tmp}<LSEP>[](symbol){count}<LEND>[statement 31; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){tmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){lower.tri}<LSEP>[](symbol){tmp}<LEND>[statement 32; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outliers}<LSEP>[](symbol){Outlier}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tmp2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){tmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outliers}<LSEP>[](symbol){Outlier}<LEND>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outliers}<LSEP>[](symbol){ind1}<LEND>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){tmp2}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outliers}<LSEP>[](symbol){ind2}<LEND>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){tmp2}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){zscore}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outliers}<LSEP>[](symbol){Outlier}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outliers}<LSEP>[](symbol){zscore}<LEND>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){zscore}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outliers}<LSEP>[](symbol){p}<LEND>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){pnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outliers}<LSEP>[](symbol){zscore}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){iqr}<LEND>[call](){}<LSEP>[](symbol){IQR}<LSEP>[](symbol){counts}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 34; assign](){<-}<LSEP>[](symbol){qth}<LEND>[call](){}<LSEP>[](symbol){quantile}<LSEP>[](symbol){counts}<LSEP>[argument 1; litteral](real){0.250000}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 35; assign](){<-}<LSEP>[](symbol){cutoff}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){qth}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){iqr}<LSEP>[](symbol){range}<LEND>[statement 36; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[argument 1; litteral](real){0.500000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[statement 37; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){counts}<LSEP>[argument 1; litteral](str){No. Pedigree Incompatable}<LSEP>[argument 2; litteral](str){steelblue}<LSEP>[argument 3; litteral](real){100.000000}<LSEP>[argument 4; litteral](NULL){NULL}<LEND>[statement 38; call](){}<LSEP>[](symbol){abline}<LSEP>[](symbol){cutoff}<LSEP>[argument 1; litteral](str){red}<LEND>[statement 39; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No outliers detected\n}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outliers}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){outliers}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outliers}<LSEP>[](symbol){Outlier}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){outliers}<LEND>[statement 40; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){op}<LEND>[statement 41; assign](){<-}<LSEP>[](symbol){hold}<LEND>[call](){}<LSEP>[](symbol){gl.drop.ind}<LSEP>[](symbol){hold}<LEND>[argument 1; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outliers}<LSEP>[](symbol){ind1}<LEND>[argument 2; litteral](real){5.000000}<LEND>[statement 42; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){rm.monomorphs}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){hold}<LEND>[call](){}<LSEP>[](symbol){gl.filter.monomorphs}<LSEP>[](symbol){hold}<LEND>[statement 43; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 44; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matdistl2dpar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){meanL}<LSEP>[](symbol){varL}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){meanL}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){meanL}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){meanL}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){matipl2dpar}<LSEP>[](symbol){meanL}<LSEP>[](symbol){varL}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){meanL}<LEND>[statement 4; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){meanL}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){meanL}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){meanL}<LEND>[body; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){j}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[statement 6; call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){distances}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){cut.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){breaks}<LSEP>[](symbol){labels}<LSEP>[](symbol){include.lowest}<LSEP>[](symbol){right}<LSEP>[](symbol){dig.lab}<LSEP>[](symbol){ordered_result}<LSEP>[](symbol){cutcol}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){cut.data.frame}<LSEP>[](symbol){x}<LSEP>[](symbol){breaks}<LSEP>[](symbol){labels}<LSEP>[](symbol){include.lowest}<LSEP>[](symbol){right}<LSEP>[](symbol){dig.lab}<LSEP>[](symbol){ordered_result}<LSEP>[](symbol){cutcol}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.folder}<LSEP>[](symbol){result}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.gene.freq}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){gl}<LSEP>[](symbol){method}<LSEP>[](symbol){stat}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){stat}<LSEP>[argument 1; litteral](str){mean}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){gl}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){tapply}<LEND>[argument 3; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){gl}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Only stat="mean" is implemen...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){t}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){selectDWD}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){name}<LSEP>[](symbol){res}<LSEP>[](symbol){var}<LSEP>[](symbol){per}<LSEP>[](symbol){base}<LSEP>[](symbol){outvec}<LSEP>[](symbol){findex}<LSEP>[](symbol){remove_dupli}<LSEP>[](symbol){current}<LSEP>[](symbol){id}<LSEP>[](symbol){mindex}<LSEP>[](symbol){exactmatch}<LSEP>[](symbol){meta}<LSEP>[](symbol){meta_txt_only}<LSEP>[](symbol){quiet}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){unused}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){unused}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){unused}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){unused}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){formals}<LSEP>[](symbol){indexFTP}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){unused}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){unused arguments in }<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){traceCall}<LEND>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LEND>[argument 2; litteral](str){: }<LEND>[argument 3; call](){}<LSEP>[](symbol){toString}<LSEP>[](symbol){unused}<LEND>[argument 4; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){findexname}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){findex}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){outvec}<LSEP>[](symbol){outvec}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){per}<LSEP>[argument 1; litteral](str){hr}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){per}<LSEP>[argument 1; litteral](str){rh}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p_index_hr}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){per}<LSEP>[argument 1; litteral](str){hr}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){p_index_hr}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p_index_hr}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){p_index_hr}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LSEP>[](symbol){p_index_hr}<LEND>[body; assign](){<-}<LSEP>[](symbol){per}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){per}<LSEP>[argument 1; litteral](str){r}<LSEP>[](symbol){i}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){per}<LSEP>[argument 1; litteral](str){hr}<LEND>[litteral](str){h}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){p_index_rh}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){per}<LSEP>[argument 1; litteral](str){rh}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){p_index_rh}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p_index_rh}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){p_index_rh}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){i}<LSEP>[](symbol){p_index_rh}<LEND>[body; assign](){<-}<LSEP>[](symbol){per}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){per}<LSEP>[argument 1; litteral](str){h}<LSEP>[](symbol){i}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){per}<LSEP>[argument 1; litteral](str){rh}<LEND>[litteral](str){r}<LEND>[statement 8; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){i}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){len}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){id}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){res}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){var}<LEND>[argument 3; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){per}<LEND>[argument 4; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){meta}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){lmin}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){id}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){res}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){var}<LEND>[argument 3; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){per}<LEND>[argument 4; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){meta}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){lmin}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){lmin}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](str){ input vectors have length zero: }<LEND>[argument 2; call](){}<LSEP>[](symbol){toString}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){id}<LSEP>[argument 1; litteral](str){res}<LSEP>[argument 2; litteral](str){var}<LSEP>[argument 3; litteral](str){per}<LSEP>[argument 4; litteral](str){meta}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){lmin}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){len}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){id}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){id}<LSEP>[](symbol){len}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){res}<LSEP>[](symbol){len}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){var}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){var}<LSEP>[](symbol){len}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){per}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){per}<LSEP>[](symbol){len}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){meta}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){meta}<LSEP>[](symbol){len}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){meta_txt_only}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){meta_txt_only}<LSEP>[](symbol){len}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){substr}<LSEP>[](symbol){per}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){h}<LEND>[litteral](str){historical}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){substr}<LSEP>[](symbol){per}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){r}<LEND>[litteral](str){recent}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){var}<LSEP>[argument 1; litteral](str){solar}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){hourly}<LSEP>[argument 1; litteral](str){daily}<LEND>[litteral](str){}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){rma}<LEND>[call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](str){multi_annual}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){rma}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id}<LSEP>[](symbol){rma}<LEND>[argument 1; litteral](str){}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){traceCall}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){: }<LEND>[argument 1; litteral](str){multi_annual data is not }<LSEP>[argument 2; litteral](str){organized by station ID. Setti...}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id}<LSEP>[](symbol){rma}<LEND>[litteral](str){}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LSEP>[](symbol){rma}<LEND>[argument 1; litteral](str){}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){traceCall}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){: }<LEND>[argument 1; litteral](str){multi_annual data is not }<LSEP>[argument 2; litteral](str){organized in period folders. S...}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LSEP>[](symbol){rma}<LEND>[litteral](str){}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){idlett}<LEND>[call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){[A-Za-z]}<LSEP>[](symbol){id}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){idlett}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){traceCall}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](str){in }<LSEP>[argument 2; litteral](str){: }<LEND>[argument 1; litteral](str){id may not contain letters: }<LEND>[argument 2; call](){}<LSEP>[](symbol){toString}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id}<LSEP>[](symbol){idlett}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 18; control flow](){if}<LSEP>[](symbol){current}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){uniquepaths}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){/}<LSEP>[](symbol){res}<LSEP>[argument 2; litteral](str){/}<LSEP>[](symbol){var}<LSEP>[argument 4; litteral](str){/}<LSEP>[](symbol){per}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){uniquepaths}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){uniquepaths}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){uniquepaths}<LSEP>[argument 1; litteral](str){///}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){uniquepaths}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){traceCall}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](str){in }<LSEP>[argument 2; litteral](str){: }<LEND>[argument 1; litteral](str){current=TRUE, but no valid pat...}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){findex}<LEND>[call](){}<LSEP>[](symbol){createIndex}<LEND>[argument 0; call](){}<LSEP>[](symbol){indexFTP}<LSEP>[](symbol){uniquepaths}<LSEP>[](symbol){base}<LSEP>[](symbol){quiet}<LSEP>[](symbol){...}<LEND>[argument 1; litteral](str){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){findexname}<LSEP>[litteral](str){currentIndex}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){id}<LEND>[call](){}<LSEP>[](symbol){suppressWarnings}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.integer}<LSEP>[](symbol){id}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){selectPrompt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){column}<LSEP>[](symbol){RES}<LSEP>[](symbol){VAR}<LSEP>[](symbol){PER}<LSEP>[](symbol){ID}<LSEP>[](symbol){index}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ID}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){ID}<LEND>[litteral](str){}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){RES}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){RES}<LEND>[litteral](str){}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){VAR}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){VAR}<LEND>[litteral](str){}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){PER}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){PER}<LEND>[litteral](str){}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){VAR}<LSEP>[argument 1; litteral](str){solar}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){RES}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){hourly}<LSEP>[argument 1; litteral](str){daily}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](str){}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){question}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){column}<LSEP>[argument 1; litteral](str){res}<LEND>[true branch; litteral](str){resolutions}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){column}<LSEP>[argument 1; litteral](str){var}<LEND>[true branch; litteral](str){variables}<LSEP>[false branch; litteral](str){periods}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){question}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Which of the following}<LSEP>[](symbol){question}<LSEP>[argument 2; litteral](str){would you like to use?}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){sid}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){ID}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){index}<LSEP>[](symbol){id}<LEND>[](symbol){ID}<LEND>[false branch; litteral](logical){TRUE}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){sres}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){RES}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){index}<LSEP>[](symbol){res}<LEND>[](symbol){RES}<LEND>[false branch; litteral](logical){TRUE}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){svar}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){VAR}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){index}<LSEP>[](symbol){var}<LEND>[](symbol){VAR}<LEND>[false branch; litteral](logical){TRUE}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){sper}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){PER}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){index}<LSEP>[](symbol){per}<LEND>[](symbol){PER}<LEND>[false branch; litteral](logical){TRUE}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){options}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){index}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){sid}<LSEP>[](symbol){sres}<LEND>[](symbol){svar}<LEND>[](symbol){sper}<LEND>[](symbol){column}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){options}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){options}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){options}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){For interactive selection, no ...}<LSEP>[argument 1; litteral](str){Proceeding with }<LSEP>[](symbol){column}<LSEP>[argument 3; litteral](str){=''.}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](str){}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){hourly}<LSEP>[](symbol){options}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){options}<LEND>[](symbol){options}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ord}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){1_minute}<LSEP>[argument 1; litteral](str){10_minutes}<LSEP>[argument 2; litteral](str){hourly}<LSEP>[argument 3; litteral](str){subdaily}<LSEP>[argument 4; litteral](str){daily}<LSEP>[argument 5; litteral](str){monthly}<LSEP>[argument 6; litteral](str){annual}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ord}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){ord}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){options}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){options}<LSEP>[](symbol){ord}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){options}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){options}<LSEP>[](symbol){ord}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){options}<LEND>[litteral](NULL){NULL}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){sel}<LEND>[call](){}<LSEP>[](symbol){menu}<LSEP>[](symbol){options}<LSEP>[](symbol){question}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){sel}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](str){}<LEND>[statement 17; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){options}<LSEP>[](symbol){sel}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){anyNA}<LSEP>[](symbol){res}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){selectPrompt}<LSEP>[argument 0; litteral](str){res}<LSEP>[](symbol){res}<LSEP>[](symbol){var}<LSEP>[](symbol){per}<LSEP>[](symbol){id}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){anyNA}<LSEP>[](symbol){var}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){var}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){var}<LEND>[call](){}<LSEP>[](symbol){selectPrompt}<LSEP>[argument 0; litteral](str){var}<LSEP>[](symbol){res}<LSEP>[](symbol){var}<LSEP>[](symbol){per}<LSEP>[](symbol){id}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){anyNA}<LSEP>[](symbol){per}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){per}<LEND>[call](){}<LSEP>[](symbol){selectPrompt}<LSEP>[argument 0; litteral](str){per}<LSEP>[](symbol){res}<LSEP>[](symbol){var}<LSEP>[](symbol){per}<LSEP>[](symbol){id}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){outwarn}<LEND>[call](){}<LSEP>[](symbol){new.env}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){len}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){givenid}<LEND>[call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){givenpath}<LEND>[call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){var}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){multi_annual}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){givenpath}<LEND>[call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){givenid}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){givenpath}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){idpath}<LEND>[litteral](str){neither station ID nor valid F...}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){base}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){givenid}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){givenpath}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){meta}<LSEP>[](symbol){i}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){idpathmeta}<LEND>[litteral](str){meta is ignored if id is given...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){filename}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){findex}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){id}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](str){path}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){filename}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){filename}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){filename}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){filename}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){id_non1_msg}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){in file index '}<LSEP>[](symbol){findexname}<LSEP>[argument 2; litteral](str){', there are }<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){id_non1_len}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){id_non1_len}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){filename}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){id_non1_ids}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){id_non1_ids}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id}<LSEP>[](symbol){i}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){/}<LSEP>[](symbol){filename}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){path}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){/}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](str){/}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){var}<LSEP>[](symbol){i}<LEND>[argument 4; litteral](str){/}<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LSEP>[](symbol){i}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){multi_annual}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){var}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){var}<LSEP>[](symbol){i}<LEND>[litteral](str){}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){sel}<LEND>[call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){var}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){var}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){per}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){per}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){sel}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_path_msg}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){according to file index '}<LSEP>[](symbol){findexname}<LSEP>[argument 2; litteral](str){', the following }<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_path_pth}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_path_pth}<LEND>[](symbol){path}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){meta}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sel}<LEND>[call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){sel}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){ismeta}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){meta_txt_only}<LSEP>[](symbol){i}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){sel}<LEND>[call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){sel}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){.pdf$}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){path}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){sel}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_desc_msg}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){according to file index '}<LSEP>[](symbol){findexname}<LSEP>[argument 2; litteral](str){', there is no description fil...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_desc_pth}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_desc_pth}<LEND>[](symbol){path}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){filename}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){findex}<LSEP>[](symbol){sel}<LSEP>[argument 2; litteral](str){path}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){/}<LSEP>[](symbol){filename}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){givenid}<LEND>[](symbol){givenpath}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){meta}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){isnotmeta}<LEND>[call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){.zip$}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){path}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){multi_annual}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){isnotmeta}<LEND>[call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){ismeta}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){sel}<LEND>[call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){sel}<LSEP>[](symbol){isnotmeta}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){filename}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){findex}<LSEP>[](symbol){sel}<LSEP>[argument 2; litteral](str){path}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){filename}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_file_msg}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){according to file index '}<LSEP>[](symbol){findexname}<LSEP>[argument 2; litteral](str){', there is no file in}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_file_pth}<LEND>[](symbol){path}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_file_pth}<LEND>[](symbol){path}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id}<LSEP>[](symbol){i}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){base}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){/}<LSEP>[](symbol){filename}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){givenid}<LSEP>[](symbol){givenpath}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){meta}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sel}<LEND>[call](){}<LSEP>[](symbol){&}<LSEP>[](symbol){sel}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){findex}<LSEP>[](symbol){id}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){sel}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_file_msg}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){according to file index '}<LSEP>[](symbol){findexname}<LSEP>[argument 2; litteral](str){', there is no file in}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_file_pth}<LEND>[](symbol){path}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_file_pth}<LEND>[](symbol){path}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id}<LSEP>[](symbol){i}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){base}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){sel}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){remove_dupli}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){filename}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){findex}<LSEP>[](symbol){sel}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){filename}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){filename}<LEND>[argument 1; call](){}<LSEP>[](symbol){which.max}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){filename}<LSEP>[](symbol){end}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){filename}<LSEP>[](symbol){start}<LEND>[argument 2; litteral](str){path}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){traceCall}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){: }<LEND>[argument 1; litteral](str){duplicate file on FTP server a...}<LSEP>[](symbol){findexname}<LSEP>[argument 3; litteral](str){'.\n - Proceeding with file wi...}<LSEP>[argument 4; litteral](str){according to time stamps in fi...}<LSEP>[argument 5; litteral](str){ - Please check actual content...}<LSEP>[argument 6; litteral](str){ - Please report this entire w...}<LSEP>[argument 7; litteral](str){https://github.com/brry/rdwd/i...}<LSEP>[](symbol){filename}<LSEP>[argument 9; litteral](logical){FALSE}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){filename}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){findex}<LSEP>[](symbol){sel}<LSEP>[argument 2; litteral](str){path}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){filename}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){traceCall}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){: }<LEND>[argument 1; litteral](str){several files (}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){filename}<LEND>[argument 3; litteral](str){) were selected:}<LEND>[argument 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){truncMessage}<LEND>[](symbol){filename}<LSEP>[argument 1; litteral](str){}<LEND>[argument 5; litteral](logical){FALSE}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){/}<LSEP>[](symbol){filename}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){truncM}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){truncMessage}<LEND>[](symbol){x}<LSEP>[argument 1; litteral](real){30.000000}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LSEP>[argument 4; litteral](str){}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){id_non1_msg}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){id_non1}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){id_non1_msg}<LEND>[argument 1; call](){}<LSEP>[](symbol){truncM}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){id_non1_len}<LEND>[argument 2; litteral](str){ files with ID }<LEND>[argument 3; call](){}<LSEP>[](symbol){truncM}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){id_non1_ids}<LEND>[statement 1; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){id_non1_msg}<LSEP>[](symbol){outwarn}<LEND>[statement 2; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){id_non1_len}<LSEP>[](symbol){outwarn}<LEND>[statement 3; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){id_non1_ids}<LSEP>[](symbol){outwarn}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_path_msg}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){missing_path_msg}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_path_pth}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_path}<LEND>[argument 1; litteral](str){ paths don't exist: }<LEND>[false branch; litteral](str){path doesn't exist: }<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_path}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_path_msg}<LEND>[](symbol){missing_path_msg}<LEND>[argument 2; call](){}<LSEP>[](symbol){truncM}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_path_pth}<LEND>[statement 2; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){miss_path_pth}<LSEP>[](symbol){outwarn}<LEND>[statement 3; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){miss_path_msg}<LSEP>[](symbol){outwarn}<LEND>[statement 29; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_desc_msg}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_desc}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_desc_msg}<LEND>[argument 1; call](){}<LSEP>[](symbol){truncM}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_desc_pth}<LEND>[statement 1; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){miss_desc_pth}<LSEP>[](symbol){outwarn}<LEND>[statement 2; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){miss_desc_msg}<LSEP>[](symbol){outwarn}<LEND>[statement 30; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_file_msg}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){missing_file}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_file_pth}<LEND>[](symbol){truncM}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){missing_file}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){'}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){missing_file}<LEND>[argument 2; litteral](str){' with ID }<LSEP>[](symbol){missing_file}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){missing_file}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){missing_file}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){\n - }<LSEP>[](symbol){missing_file}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_file}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outwarn}<LSEP>[](symbol){miss_file_msg}<LEND>[argument 1; litteral](str){ }<LEND>[argument 2; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){missing_file}<LSEP>[argument 1; litteral](str){}<LEND>[argument 3; litteral](str){.}<LEND>[statement 4; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){miss_file_pth}<LSEP>[](symbol){outwarn}<LEND>[statement 5; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){miss_file_msg}<LSEP>[](symbol){outwarn}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){outwarn}<LEND>[call](){}<LSEP>[](symbol){as.list}<LSEP>[](symbol){outwarn}<LEND>[statement 32; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){outwarn}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){traceCall}<LEND>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){: }<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){outwarn}<LSEP>[argument 1; litteral](str){\n}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){output}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){len}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){output}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){output}<LEND>[statement 34; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){len}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){outvec}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){output}<LEND>[statement 35; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){output}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){getRversion}<LEND>[argument 1; litteral](str){2.15.1}<LEND>[true branch; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){utils}<LSEP>[](symbol){globalVariables}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){id_non1_ids}<LSEP>[argument 1; litteral](str){id_non1_len}<LSEP>[argument 2; litteral](str){id_non1_msg}<LSEP>[argument 3; litteral](str){miss_desc_msg}<LSEP>[argument 4; litteral](str){miss_desc_pth}<LSEP>[argument 5; litteral](str){miss_file_msg}<LSEP>[argument 6; litteral](str){miss_file_pth}<LSEP>[argument 7; litteral](str){miss_path_msg}<LSEP>[argument 8; litteral](str){miss_path_pth}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.sim.offspring}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fathers}<LSEP>[](symbol){mothers}<LSEP>[](symbol){noffpermother}<LSEP>[](symbol){sexratio}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){noff}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){mothers}<LEND>[](symbol){noffpermother}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mother}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){mothers}<LEND>[](symbol){noff}<LSEP>[](symbol){T}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){father}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){fathers}<LEND>[](symbol){noff}<LSEP>[](symbol){T}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){mmat}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){mothers}<LEND>[](symbol){mother}<LSEP>[](symbol){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mhet}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mmat}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){mhet}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mother.half}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mmat}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){mhet}<LSEP>[](symbol){T}<LEND>[](symbol){mmat}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mother.half}<LSEP>[](symbol){mmat}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){fmat}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){fathers}<LEND>[](symbol){father}<LSEP>[](symbol){}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){fhet}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){fmat}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){fhet}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){father.half}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){fmat}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){fhet}<LSEP>[](symbol){T}<LEND>[](symbol){fmat}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){father.half}<LSEP>[](symbol){fmat}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){offmat}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mother.half}<LSEP>[](symbol){father.half}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){gl2}<LEND>[call](){}<LSEP>[](symbol){new}<LSEP>[argument 0; litteral](str){genlight}<LSEP>[](symbol){offmat}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Po_}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){noff}<LEND>[argument 3; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){mothers}<LEND>[argument 4; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){offmat}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){sr}<LEND>[call](){}<LSEP>[](symbol){factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){runif}<LEND>[argument 0; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){gl2}<LEND>[](symbol){sexratio}<LEND>[argument 1; litteral](str){female}<LSEP>[argument 2; litteral](str){male}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl2}<LSEP>[](symbol){other}<LEND>[](symbol){sex}<LEND>[](symbol){sr}<LEND>[statement 13; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){gl2}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plot.fpcad}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){nscore}<LSEP>[](symbol){main}<LSEP>[](symbol){sub.title}<LSEP>[](symbol){color}<LSEP>[](symbol){fontsize.points}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nscore}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Since dad-4, nscore must be a ...}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){and}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 4; litteral](str){are plotted.}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nscore}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){inertia}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){inertia}<LEND>[](symbol){inertia}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){coor}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){scores}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nscore}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){nscore}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){nscore}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){coor}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The components of nscore must ...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){color}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){coor}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){coor}<LSEP>[](symbol){color}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){group}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){scores}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 8; assign](){=}<LSEP>[](symbol){i1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){i2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){ggplot}<LSEP>[](symbol){coor}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes_q}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.name}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){coor}<LEND>[](symbol){i1}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.name}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){coor}<LEND>[](symbol){i2}<LEND>[argument 2; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){group}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){color}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes}<LEND>[argument 0; call](){}<LSEP>[](symbol){I}<LSEP>[](symbol){color}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_text}<LSEP>[argument 0; litteral](str){bold}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){4.200000}<LSEP>[](symbol){fontsize.points}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){labs}<LSEP>[](symbol){main}<LSEP>[](symbol){sub.title}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){coor}<LEND>[](symbol){i1}<LEND>[argument 1; litteral](str){ (}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){inertia}<LSEP>[](symbol){i1}<LEND>[argument 3; litteral](str){%)}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){coor}<LEND>[](symbol){i2}<LEND>[argument 1; litteral](str){ (}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){inertia}<LSEP>[](symbol){i2}<LEND>[argument 3; litteral](str){%)}<LEND>[statement 15; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){graph}<LEND>[statement 16; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.report.reproducibility}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){boxplot}<LSEP>[](symbol){range}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Fatal Error: genlight object...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence ...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Terminating Execution!}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){hold}<LSEP>[](symbol){x}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){repeatability}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){RepAvg}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){repeatability}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){Reproducibility}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){xlimit}<LEND>[call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){repeatability}<LEND>[statement 10; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of loci =}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 11; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of individuals =}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 12; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Miniumum repeatability: }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){repeatability}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 13; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Maximum repeatability: }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){repeatability}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 14; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Mean repeatability: }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){repeatability}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){retained}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){21.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){pc.retained}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){21.000000}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){filtered}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){21.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){pc.filtered}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){21.000000}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){percentile}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){21.000000}<LEND>[statement 20; control flow](){for}<LSEP>[](symbol){index}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){21.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){index}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){20.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){xlimit}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){percentile}<LSEP>[](symbol){index}<LEND>[](symbol){i}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){retained}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){repeatability}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){repeatability}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){percentile}<LSEP>[](symbol){index}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pc.retained}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){retained}<LSEP>[](symbol){index}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){filtered}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){retained}<LSEP>[](symbol){index}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pc.filtered}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pc.retained}<LSEP>[](symbol){index}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){percentile}<LSEP>[](symbol){retained}<LSEP>[](symbol){pc.retained}<LSEP>[](symbol){filtered}<LSEP>[](symbol){pc.filtered}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){df}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Threshold}<LSEP>[argument 1; litteral](str){Retained}<LSEP>[argument 2; litteral](str){Percent}<LSEP>[argument 3; litteral](str){Filtered}<LSEP>[argument 4; litteral](str){Percent}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Threshold}<LEND>[](symbol){}<LEND>[statement 25; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){df}<LEND>[litteral](NULL){NULL}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){op}<LEND>[call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[argument 1; litteral](real){0.500000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[argument 3; litteral](str){m}<LEND>[statement 27; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.500000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){title}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){SNP data (DArTSeq)\nRepeatbili...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){title}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Fragment P/A data (SilicoDArT)...}<LEND>[statement 29; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){boxplot}<LSEP>[argument 1; litteral](str){standard}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){boxplot}<LSEP>[](symbol){repeatability}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){red}<LSEP>[](symbol){range}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){repeatability}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){title}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Standard boxplot, no adjustmen...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){robustbase}<LSEP>[](symbol){adjbox}<LEND>[](symbol){repeatability}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){red}<LSEP>[](symbol){range}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){repeatability}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){title}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Boxplot adjusted to account fo...}<LEND>[statement 30; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[argument 1; litteral](real){0.500000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[statement 31; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){repeatability}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){red}<LEND>[argument 4; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){repeatability}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 5; litteral](real){100.000000}<LEND>[statement 32; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){op}<LEND>[statement 33; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 34; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){df}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matddlppar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){freq}<LSEP>[](symbol){p}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){freq}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){freq}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){freq}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){freq}<LEND>[body; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){freq}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){freq}<LSEP>[](symbol){j}<LEND>[](symbol){p}<LEND>[statement 3; call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){distances}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.smart_import_rrd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){filename}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){assert_that}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){filename}<LEND>[statement 1; call](){}<LSEP>[](symbol){assert_that}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.exists}<LSEP>[](symbol){filename}<LEND>[statement 2; call](){.Call}<LSEP>[call name; litteral](str){smart_import_rrd}<LSEP>[](symbol){filename}<LSEP>[argument 1; litteral](str){rrd}<LEND>[assign](){<-}<LSEP>[](symbol){.import_rrd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){filename}<LSEP>[](symbol){cf}<LSEP>[](symbol){start}<LSEP>[](symbol){end}<LSEP>[](symbol){step}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){assert_that}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){filename}<LEND>[statement 1; call](){}<LSEP>[](symbol){assert_that}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.exists}<LSEP>[](symbol){filename}<LEND>[statement 2; call](){.Call}<LSEP>[call name; litteral](str){import_rrd}<LSEP>[](symbol){filename}<LSEP>[](symbol){cf}<LSEP>[](symbol){start}<LSEP>[](symbol){end}<LSEP>[](symbol){step}<LSEP>[argument 5; litteral](str){rrd}<LEND>[assign](){<-}<LSEP>[](symbol){.describe_rrd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){filename}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){assert_that}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){filename}<LEND>[statement 1; call](){}<LSEP>[](symbol){assert_that}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.exists}<LSEP>[](symbol){filename}<LEND>[statement 2; call](){.Call}<LSEP>[call name; litteral](str){describe_rrd}<LSEP>[](symbol){filename}<LSEP>[argument 1; litteral](str){rrd}<LEND>[statement 3; litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){print.fpcad}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){mean.print}<LSEP>[](symbol){var.print}<LSEP>[](symbol){cor.print}<LSEP>[](symbol){skewness.print}<LSEP>[](symbol){kurtosis.print}<LSEP>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){group variable: }<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){variables: }<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variables}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){inertia\n}<LEND>[statement 4; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){inertia}<LEND>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){...}<LEND>[statement 5; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){contributions\n}<LEND>[statement 7; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){contributions}<LEND>[](symbol){...}<LEND>[statement 8; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){qualities\n}<LEND>[statement 10; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){qualities}<LEND>[](symbol){...}<LEND>[statement 11; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 12; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){scores\n}<LEND>[statement 13; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){scores}<LEND>[](symbol){...}<LEND>[statement 14; control flow](){if}<LSEP>[](symbol){mean.print}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n.group}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){means}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){n.var}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){means}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){Means}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){means}<LEND>[](symbol){n.group}<LSEP>[](symbol){n.var}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[argument 4; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](NULL){NULL}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){mean}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variables}<LEND>[argument 2; litteral](str){.}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){Means}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){means}<LEND>[](symbol){Means}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 4; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){Means}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){contributions}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){n.var}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){st.dev}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variances}<LEND>[](symbol){diag}<LEND>[](symbol){sqrt}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){st.dev}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variances}<LEND>[](symbol){sqrt}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){Means}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){Means}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){st.dev}<LSEP>[](symbol){n.group}<LSEP>[](symbol){n.var}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[argument 4; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](NULL){NULL}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){sd}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variables}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){Means}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){Means}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){norm}<LEND>[](symbol){norm}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 8; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){means, standard deviations and...}<LEND>[statement 10; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){Means}<LSEP>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 15; control flow](){if}<LSEP>[](symbol){var.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){variances/covariances by group\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variances}<LEND>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 16; control flow](){if}<LSEP>[](symbol){cor.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){correlations by group\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){correlations}<LEND>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 17; control flow](){if}<LSEP>[](symbol){skewness.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){skewness coefficients by group\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){skewness}<LEND>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 18; control flow](){if}<LSEP>[](symbol){kurtosis.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){kurtosis coefficients by group\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){kurtosis}<LEND>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 19; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.percent.freq}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Monomorphic loci reta...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){seppop}<LSEP>[](symbol){x}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){x2_list}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){x2}<LSEP>[](symbol){as.matrix}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SilicoDArT}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting gl.percent.freq: Calc...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x2_list}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){x2_list}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting gl.percent.freq: Calc...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ This may take some time -- b...}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){loc_names}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){x2_list}<LSEP>[](symbol){colnames}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){nmissing_temp}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){x2_list}<LSEP>[](symbol){is.na}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){nmissing}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){nmissing_temp}<LSEP>[](symbol){colSums}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){n_temp}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){x2_list}<LSEP>[](symbol){nrow}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){n_temp}<LSEP>[](symbol){rep}<LEND>[argument 2; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){nobs_temp}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){nmissing}<LSEP>[](symbol){unname}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){nobs}<LEND>[call](){}<LSEP>[](symbol){Map}<LSEP>[argument 0; litteral](str){-}<LSEP>[](symbol){n}<LSEP>[](symbol){nobs_temp}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){sum_res}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){x2_list}<LSEP>[](symbol){colSums}<LSEP>[](symbol){T}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){x2_list}<LSEP>[](symbol){colMeans}<LSEP>[](symbol){T}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){/}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){*}<LSEP>[argument 2; litteral](real){100.000000}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](str){round}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){Map}<LSEP>[](symbol){cbind}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){sum_res}<LEND>[](symbol){loc_names}<LSEP>[](symbol){sum_res}<LSEP>[](symbol){nobs}<LSEP>[](symbol){nmissing}<LSEP>[](symbol){f}<LSEP>[](symbol){n}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){m}<LSEP>[](symbol){cbind}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){m}<LSEP>[](symbol){as.data.frame}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){rbind.fill}<LSEP>[](symbol){m}<LEND>[statement 27; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){popn}<LSEP>[argument 1; litteral](str){locus}<LSEP>[argument 2; litteral](str){sum}<LSEP>[argument 3; litteral](str){nobs}<LSEP>[argument 4; litteral](str){nmissing}<LSEP>[argument 5; litteral](str){frequency}<LSEP>[argument 6; litteral](str){n}<LSEP>[argument 7; litteral](str){loc_order}<LEND>[statement 28; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){popn}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){popn}<LEND>[statement 29; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){locus}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){locus}<LEND>[statement 30; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){sum}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){sum}<LEND>[statement 31; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){nobs}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){nobs}<LEND>[statement 32; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){nmissing}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){nmissing}<LEND>[statement 33; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){frequency}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){frequency}<LEND>[statement 34; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){n}<LEND>[statement 35; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){loc_order}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){loc_order}<LEND>[statement 36; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){loc_order}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){popn}<LEND>[](symbol){}<LEND>[statement 37; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){m}<LEND>[statement 38; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){m}<LEND>[litteral](NULL){NULL}<LEND>[statement 39; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 40; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){m}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){print.rrat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Robust Regression with Asymmet...}<LSEP>[argument 1; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){taus: }<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){taus}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Bias Correction: }<LEND>[argument 1; call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bias_correction}<LEND>[argument 1; litteral](real){4.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Coefficients: \n}<LEND>[statement 5; call](){}<LSEP>[](symbol){print.default}<LEND>[argument 0; call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){rrat_coefficients}<LEND>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](integer){2}<LSEP>[argument 2; litteral](logical){FALSE}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){ntrm_ared}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){nu}<LSEP>[](symbol){f_current}<LSEP>[](symbol){f_candidate}<LSEP>[](symbol){s_current}<LSEP>[](symbol){s_candidate}<LSEP>[](symbol){m0_current}<LSEP>[](symbol){m0_candidate}<LSEP>[](symbol){mu}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){ntrm_merit}<LSEP>[](symbol){nu}<LSEP>[](symbol){f_current}<LSEP>[](symbol){s_current}<LSEP>[](symbol){m0_current}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){ntrm_merit}<LSEP>[](symbol){nu}<LSEP>[](symbol){f_candidate}<LSEP>[](symbol){s_candidate}<LSEP>[](symbol){m0_candidate}<LSEP>[](symbol){mu}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_create_constraints}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){upper_bound}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){idx_lb}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){lower_bound}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){idx_ub}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){upper_bound}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lower_bound}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){m_lb}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){idx_lb}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){m_ub}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){idx_ub}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){m_lb}<LSEP>[](symbol){m_ub}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){A}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){m}<LSEP>[](symbol){n}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){m_lb}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){idx_lb}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){m_lb}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){idx_ub}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 9; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){idx_lb}<LSEP>[](symbol){idx_ub}<LSEP>[](symbol){A}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_error}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){obj}<LSEP>[](symbol){mu}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){ntrm_max_abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){G}<LEND>[argument 1; call](){}<LSEP>[](symbol){crossprod}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){ntrm_max_abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){s}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){z}<LEND>[](symbol){mu}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m0}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_inertia_correction}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){H}<LSEP>[](symbol){A}<LSEP>[](symbol){slack_variable}<LSEP>[](symbol){lagrange_multiplier}<LSEP>[](symbol){kappa}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eps}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){n_variables}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){A}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){n_constraints}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){A}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){n_slacks}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){slack_variable}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){n_total}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n_variables}<LSEP>[](symbol){n_constraints}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){idx}<LEND>[call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){n_total}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){X}<LEND>[call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){H}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){n_variables}<LSEP>[](symbol){n_slacks}<LEND>[argument 2; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){n_slacks}<LSEP>[](symbol){n_variables}<LEND>[argument 1; call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){lagrange_multiplier}<LSEP>[](symbol){slack_variable}<LEND>[](symbol){n_slacks}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){n_slacks}<LEND>[argument 2; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){n_slacks}<LEND>[argument 2; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){n_constraints}<LSEP>[](symbol){n_constraints}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){eigval}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){eigen}<LSEP>[](symbol){X}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[](symbol){values}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){some_zero}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){eigval}<LEND>[](symbol){eps}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){some_negative}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eigval}<LSEP>[](symbol){idx}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){eps}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){some_positive}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eigval}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){idx}<LEND>[](symbol){eps}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LSEP>[](symbol){some_zero}<LSEP>[](symbol){some_negative}<LEND>[](symbol){some_positive}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){kappa}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){kappa}<LSEP>[litteral](real){0.000100}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){kappa}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){kappa}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; control flow](){repeat}<LSEP>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){X}<LEND>[call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){H}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){kappa}<LEND>[argument 1; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){n_variables}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){n_variables}<LSEP>[](symbol){n_slacks}<LEND>[argument 2; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){n_slacks}<LSEP>[](symbol){n_variables}<LEND>[argument 1; call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){lagrange_multiplier}<LSEP>[](symbol){slack_variable}<LEND>[](symbol){n_slacks}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){n_slacks}<LEND>[argument 2; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){n_slacks}<LEND>[argument 2; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){n_constraints}<LSEP>[](symbol){n_constraints}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){eigval}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){eigen}<LSEP>[](symbol){X}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[](symbol){values}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){some_zero}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){eigval}<LEND>[](symbol){eps}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){some_negative}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eigval}<LSEP>[](symbol){idx}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){eps}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){some_positive}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eigval}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){idx}<LEND>[](symbol){eps}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LSEP>[](symbol){some_zero}<LSEP>[](symbol){some_negative}<LEND>[](symbol){some_positive}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){kappa}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[](symbol){kappa}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){break}<LEND>[](symbol){kappa}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_init_obj}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fn}<LSEP>[](symbol){gh}<LSEP>[](symbol){C}<LSEP>[](symbol){x}<LSEP>[](symbol){s}<LSEP>[](symbol){A}<LSEP>[](symbol){mu}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n_var}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){A}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){n_slk}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){A}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){n_tot}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n_var}<LSEP>[](symbol){n_slk}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){obj}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){A}<LSEP>[](symbol){n_var}<LSEP>[](symbol){n_slk}<LEND>[argument 3; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n_var}<LSEP>[](symbol){n_slk}<LEND>[argument 4; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){n_var}<LEND>[argument 5; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n_var}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n_tot}<LEND>[](symbol){x}<LEND>[argument 7; call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){x}<LEND>[](symbol){s}<LEND>[argument 9; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){C}<LSEP>[](symbol){x}<LEND>[](symbol){s}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m0}<LEND>[call](){}<LSEP>[](symbol){ntrm_norm}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){r}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){gradient_hessian}<LEND>[call](){}<LSEP>[](symbol){gh}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){x}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){G}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gradient_hessian}<LSEP>[](symbol){G}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){H}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gradient_hessian}<LSEP>[](symbol){H}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){B}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){s}<LSEP>[](symbol){n_slk}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){Y}<LEND>[call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){n_tot}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){n_slk}<LSEP>[](symbol){n_slk}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){u}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){G}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){ntrm_lagrange_multiplier}<LSEP>[](symbol){obj}<LSEP>[](symbol){mu}<LEND>[](symbol){obj}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_lagrange_multiplier}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){obj}<LSEP>[](symbol){mu}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){idx_z}<LEND>[call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){n}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){n}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){b}<LSEP>[](symbol){idx_z}<LEND>[call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){u}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){Y}<LEND>[](symbol){b}<LEND>[](symbol){idx_z}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){idx_neg}<LEND>[call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){z}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){idx_neg}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){z}<LSEP>[](symbol){idx_neg}<LEND>[call](){}<LSEP>[](symbol){pmin}<LSEP>[argument 0; litteral](real){0.001000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){s}<LEND>[](symbol){idx_neg}<LEND>[](symbol){z}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_merit}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){nu}<LSEP>[](symbol){f}<LSEP>[](symbol){s}<LSEP>[](symbol){m0}<LSEP>[](symbol){mu}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){f}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){s}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){nu}<LSEP>[](symbol){m0}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_objective_function}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){Q}<LSEP>[](symbol){u}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){0.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){Q}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p}<LSEP>[](symbol){u}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_pred}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){nu}<LSEP>[](symbol){m0}<LSEP>[](symbol){mp}<LSEP>[](symbol){h}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){nu}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){m0}<LSEP>[](symbol){mp}<LEND>[](symbol){h}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_reductions}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){obj}<LSEP>[](symbol){candidate}<LSEP>[](symbol){mu}<LSEP>[](symbol){nu}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nu}<LEND>[call](){}<LSEP>[](symbol){ntrm_update_nu}<LSEP>[](symbol){nu}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){h}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m0}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){mp}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ared}<LEND>[call](){}<LSEP>[](symbol){ntrm_ared}<LSEP>[](symbol){nu}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){f}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){f}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){s}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){s}<LEND>[argument 5; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m0}<LEND>[argument 6; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){m0}<LEND>[](symbol){mu}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){pred}<LEND>[call](){}<LSEP>[](symbol){ntrm_pred}<LSEP>[](symbol){nu}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m0}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){mp}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){h}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){rho}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){ared}<LSEP>[](symbol){pred}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){rho}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rho}<LSEP>[litteral](real){0.000000}<LEND>[statement 5; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){nu}<LSEP>[](symbol){ared}<LSEP>[](symbol){pred}<LSEP>[](symbol){rho}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_step}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){obj}<LSEP>[](symbol){delta}<LSEP>[](symbol){tau}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){v}<LEND>[call](){}<LSEP>[](symbol){ntrm_step_normal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){Y}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){B}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){r}<LEND>[](symbol){delta}<LSEP>[](symbol){tau}<LEND>[argument 5; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){idx_s}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mp}<LEND>[call](){}<LSEP>[](symbol){ntrm_norm}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){B}<LEND>[](symbol){v}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){r}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){kappa}<LEND>[call](){}<LSEP>[](symbol){ntrm_inertia_correction}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){H}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){A}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){s}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){z}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){kappa}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){V}<LEND>[call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){s}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){Q}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){n}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){n}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Q}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){k}<LEND>[argument 2; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){H}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){kappa}<LEND>[argument 1; call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){k}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Q}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){k}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){n}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){k}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){n}<LEND>[](symbol){V}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){step}<LEND>[call](){}<LSEP>[](symbol){ntrm_step_tilde}<LSEP>[](symbol){Q}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){u}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){B}<LEND>[](symbol){v}<LSEP>[](symbol){delta}<LSEP>[](symbol){tau}<LEND>[argument 6; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){idx_s}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){step}<LSEP>[](symbol){p}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){idx_s}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){s}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){idx_s}<LEND>[statement 10; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){idx_x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){idx_s}<LEND>[argument 2; call](){}<LSEP>[](symbol){ntrm_norm}<LSEP>[](symbol){p}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){step}<LSEP>[](symbol){h}<LEND>[](symbol){mp}<LSEP>[](symbol){kappa}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_step_normal}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Y}<LSEP>[](symbol){B}<LSEP>[](symbol){slack_residual}<LSEP>[](symbol){delta}<LSEP>[](symbol){tau}<LSEP>[](symbol){idx_s}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rho}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){0.800000}<LSEP>[](symbol){delta}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){omega}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){tau}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){B}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){slack_residual}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){v_gn}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){Y}<LSEP>[](symbol){b}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){n}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){v_gn_norm}<LEND>[call](){}<LSEP>[](symbol){ntrm_norm}<LSEP>[](symbol){v_gn}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){v}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){v_gn_norm}<LSEP>[](symbol){rho}<LEND>[true branch; block](){}<LSEP>[](symbol){v_gn}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){crossprod}<LSEP>[](symbol){B}<LSEP>[](symbol){slack_residual}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){v_sd}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){g}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){B}<LSEP>[](symbol){g}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){g}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){v_sd_norm}<LEND>[call](){}<LSEP>[](symbol){ntrm_norm}<LSEP>[](symbol){v_sd}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){v_sd_norm}<LSEP>[](symbol){rho}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){rho}<LSEP>[](symbol){v_sd_norm}<LEND>[](symbol){v_sd}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){v_gn}<LSEP>[](symbol){v_sd}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){ntrm_solve_quadratic_equation}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){x}<LSEP>[](symbol){v_sd}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){v_sd_norm}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){delta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){v_gn}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){v_sd}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){small_v}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v}<LSEP>[](symbol){idx_s}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){small_v}<LSEP>[](symbol){omega}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){v}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){omega}<LSEP>[](symbol){small_v}<LEND>[](symbol){v}<LEND>[](symbol){v}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_step_shrink}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){a}<LSEP>[](symbol){d}<LSEP>[](symbol){tau}<LSEP>[](symbol){idx_s}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p_new}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){a}<LSEP>[](symbol){d}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){which.min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p_new}<LSEP>[](symbol){idx_s}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){small_p}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p_new}<LSEP>[](symbol){idx_s}<LEND>[](symbol){i}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){small_p}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){tau}<LEND>[true branch; block](){}<LSEP>[](symbol){a}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){small_d}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){d}<LSEP>[](symbol){idx_s}<LEND>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){a_shrink}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){tau}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){idx_s}<LEND>[](symbol){i}<LEND>[](symbol){small_d}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){a_shrink}<LEND>[argument 1; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){a}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[](symbol){a_shrink}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_step_tilde}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Q}<LSEP>[](symbol){u}<LSEP>[](symbol){B}<LSEP>[](symbol){initial_value}<LSEP>[](symbol){delta}<LSEP>[](symbol){tau}<LSEP>[](symbol){idx_s}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eps}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){B}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){B}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){K}<LEND>[call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){Q}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){m}<LSEP>[](symbol){m}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){p}<LEND>[assign](){<-}<LSEP>[](symbol){p_new}<LEND>[assign](){<-}<LSEP>[](symbol){p_old}<LSEP>[](symbol){initial_value}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){h}<LEND>[call](){}<LSEP>[](symbol){ntrm_objective_function}<LSEP>[](symbol){p}<LSEP>[](symbol){Q}<LSEP>[](symbol){u}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){Q}<LSEP>[](symbol){p_old}<LEND>[](symbol){u}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){m}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){K}<LSEP>[](symbol){b}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){n}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){dot}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LSEP>[](symbol){g}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){g}<LEND>[statement 11; control flow](){repeat}<LSEP>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){Q}<LSEP>[](symbol){d}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dqf}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){d}<LSEP>[](symbol){W}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){dot}<LSEP>[](symbol){dqf}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){p_new}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p_old}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){a}<LSEP>[](symbol){d}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){dqf}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p_new_norm}<LEND>[call](){}<LSEP>[](symbol){ntrm_norm}<LSEP>[](symbol){p_new}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p_new_norm}<LSEP>[](symbol){delta}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k_sol}<LEND>[call](){}<LSEP>[](symbol){ntrm_solve_quadratic_equation}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){d}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){d}<LSEP>[](symbol){p_old}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){p_old}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){delta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){k}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){k_sol}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){k_sol}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){a_shrink}<LEND>[call](){}<LSEP>[](symbol){ntrm_step_shrink}<LSEP>[](symbol){p_old}<LSEP>[](symbol){k}<LSEP>[](symbol){d}<LSEP>[](symbol){tau}<LSEP>[](symbol){idx_s}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){a_shrink}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p_tmp}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p_old}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){a_shrink}<LSEP>[](symbol){d}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){hs}<LEND>[call](){}<LSEP>[](symbol){ntrm_objective_function}<LSEP>[](symbol){p_tmp}<LSEP>[](symbol){Q}<LSEP>[](symbol){u}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){hs}<LSEP>[](symbol){h}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LSEP>[](symbol){p_tmp}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){h}<LSEP>[](symbol){hs}<LEND>[statement 4; control flow](){break}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[](symbol){dqf}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){Q}<LSEP>[](symbol){p_old}<LEND>[](symbol){u}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){ntrm_solve_quadratic_equation}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){d}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){d}<LSEP>[](symbol){p_old}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){p_old}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){delta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){ntrm_line_search}<LSEP>[](symbol){f}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){ntrm_step_shrink}<LSEP>[](symbol){p_old}<LSEP>[](symbol){a}<LSEP>[](symbol){d}<LSEP>[](symbol){tau}<LSEP>[](symbol){idx_s}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p_tmp}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p_old}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){a}<LSEP>[](symbol){d}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){hs}<LEND>[call](){}<LSEP>[](symbol){ntrm_objective_function}<LSEP>[](symbol){p_tmp}<LSEP>[](symbol){Q}<LSEP>[](symbol){u}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){hs}<LSEP>[](symbol){h}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LSEP>[](symbol){p_tmp}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){h}<LSEP>[](symbol){hs}<LEND>[statement 5; control flow](){break}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){a_shrink}<LEND>[call](){}<LSEP>[](symbol){ntrm_step_shrink}<LSEP>[](symbol){p_old}<LSEP>[](symbol){a}<LSEP>[](symbol){d}<LSEP>[](symbol){tau}<LSEP>[](symbol){idx_s}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){a_shrink}<LSEP>[](symbol){a}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LSEP>[](symbol){p_new}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){h}<LEND>[call](){}<LSEP>[](symbol){ntrm_objective_function}<LSEP>[](symbol){p}<LSEP>[](symbol){Q}<LSEP>[](symbol){u}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){a_shrink}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p_tmp}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p_old}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){a_shrink}<LSEP>[](symbol){d}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){hs}<LEND>[call](){}<LSEP>[](symbol){ntrm_objective_function}<LSEP>[](symbol){p_tmp}<LSEP>[](symbol){Q}<LSEP>[](symbol){u}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){hs}<LSEP>[](symbol){h}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LSEP>[](symbol){p_tmp}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){h}<LSEP>[](symbol){hs}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){converged}<LEND>[call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){ntrm_max_abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p_new}<LSEP>[](symbol){p_old}<LEND>[argument 1; call](){}<LSEP>[](symbol){ntrm_max_abs}<LSEP>[](symbol){p_new}<LEND>[](symbol){eps}<LEND>[statement 8; control flow](){if}<LSEP>[](symbol){converged}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){break}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){a}<LSEP>[](symbol){W}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){m}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){K}<LSEP>[](symbol){b}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){n}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){dot_old}<LSEP>[](symbol){dot}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){dot}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){r}<LSEP>[](symbol){g}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){dot}<LEND>[](symbol){eps}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){break}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){p_old}<LSEP>[](symbol){p_new}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){g}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){dot}<LSEP>[](symbol){dot_old}<LEND>[](symbol){d}<LEND>[statement 12; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){p}<LSEP>[](symbol){h}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_update_nu}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){nu}<LSEP>[](symbol){h}<LSEP>[](symbol){m0}<LSEP>[](symbol){mp}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){denominator}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){0.700000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){m0}<LSEP>[](symbol){mp}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){denominator}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; block](){}<LSEP>[](symbol){nu}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nu_lb}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){h}<LSEP>[](symbol){denominator}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){nu_lb}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){nu_lb}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){nu}<LSEP>[](symbol){nu_lb}<LEND>[true branch; block](){}<LSEP>[](symbol){nu}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nu_lb}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_update_solution}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){obj}<LSEP>[](symbol){candidate}<LSEP>[](symbol){gh}<LSEP>[](symbol){mu}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){f}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){s}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){s}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){r}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m0}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){m0}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){gradient_hessian}<LEND>[call](){}<LSEP>[](symbol){gh}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){x}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){G}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gradient_hessian}<LSEP>[](symbol){G}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){H}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gradient_hessian}<LSEP>[](symbol){H}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){B}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){s}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){Y}<LEND>[call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){B}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){u}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){G}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){ntrm_lagrange_multiplier}<LSEP>[](symbol){obj}<LSEP>[](symbol){mu}<LEND>[](symbol){obj}<LEND>[assign](){<-}<LSEP>[](symbol){ntrm_constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fn}<LSEP>[](symbol){gh}<LSEP>[](symbol){init}<LSEP>[](symbol){max_iter}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){upper_bound}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eps_1}<LSEP>[litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){eps_2}<LSEP>[litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){eps_counter}<LSEP>[litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){delta}<LSEP>[litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mu}<LSEP>[litteral](real){0.100000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){eta}<LSEP>[litteral](real){0.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tau}<LSEP>[litteral](real){0.995000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){nu}<LSEP>[litteral](real){0.500000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){converged}<LSEP>[litteral](logical){FALSE}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){constraints}<LEND>[call](){}<LSEP>[](symbol){ntrm_create_constraints}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){upper_bound}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){il}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){constraints}<LSEP>[](symbol){idx_lb}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){iu}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){constraints}<LSEP>[](symbol){idx_ub}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){lb}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){il}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){ub}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upper_bound}<LSEP>[](symbol){iu}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){C}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){il}<LEND>[](symbol){lb}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ub}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){iu}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){cur_optimum}<LSEP>[](symbol){init}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){is_out}<LEND>[call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){init}<LSEP>[](symbol){lower_bound}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){init}<LSEP>[](symbol){upper_bound}<LEND>[statement 17; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){constraints}<LSEP>[](symbol){A}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){is_out}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.infinite}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cur_optimum}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upper_bound}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.infinite}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upper_bound}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cur_optimum}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cur_optimum}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){upper_bound}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){s}<LEND>[call](){}<LSEP>[](symbol){tryCatch}<LEND>[argument 0; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){ntrm_line_search}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){slacks}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){constraints}<LSEP>[](symbol){A}<LEND>[statement 1; call](){}<LSEP>[](symbol){ntrm_error}<LEND>[argument 0; call](){}<LSEP>[](symbol){ntrm_init_obj}<LSEP>[](symbol){fn}<LSEP>[](symbol){gh}<LSEP>[](symbol){C}<LSEP>[](symbol){cur_optimum}<LSEP>[](symbol){slacks}<LEND>[argument 5; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){constraints}<LSEP>[](symbol){A}<LEND>[](symbol){mu}<LEND>[](symbol){mu}<LEND>[argument 1; litteral](real){0.010000}<LSEP>[argument 2; litteral](real){100.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){e}<LEND>[body; block](){}<LSEP>[statement 0; litteral](real){1.000000}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){obj}<LEND>[call](){}<LSEP>[](symbol){ntrm_init_obj}<LSEP>[](symbol){fn}<LSEP>[](symbol){gh}<LSEP>[](symbol){C}<LSEP>[](symbol){cur_optimum}<LEND>[argument 4; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){s}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){constraints}<LSEP>[](symbol){A}<LEND>[argument 5; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){constraints}<LSEP>[](symbol){A}<LEND>[](symbol){mu}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){error}<LEND>[call](){}<LSEP>[](symbol){ntrm_error}<LSEP>[](symbol){obj}<LSEP>[](symbol){mu}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){error}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){obj}<LEND>[call](){}<LSEP>[](symbol){ntrm_init_obj}<LSEP>[](symbol){fn}<LSEP>[](symbol){gh}<LSEP>[](symbol){C}<LSEP>[](symbol){cur_optimum}<LEND>[argument 4; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){constraints}<LSEP>[](symbol){A}<LEND>[argument 5; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){constraints}<LSEP>[](symbol){A}<LEND>[](symbol){mu}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){i}<LSEP>[litteral](real){0.000000}<LEND>[statement 23; control flow](){repeat}<LSEP>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){error}<LEND>[call](){}<LSEP>[](symbol){ntrm_error}<LSEP>[](symbol){obj}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){error}<LSEP>[](symbol){eps_1}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){converged}<LSEP>[litteral](logical){TRUE}<LEND>[statement 1; control flow](){break}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){error}<LSEP>[](symbol){eps_2}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){eps_counter}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){converged}<LSEP>[litteral](logical){TRUE}<LEND>[statement 1; control flow](){break}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eps_counter}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){eps_counter}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){i}<LSEP>[](symbol){max_iter}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){break}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){kappa}<LEND>[litteral](real){0.000000}<LEND>[statement 4; control flow](){repeat}<LSEP>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){error}<LEND>[call](){}<LSEP>[](symbol){ntrm_error}<LSEP>[](symbol){obj}<LSEP>[](symbol){mu}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){error}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){delta}<LSEP>[](symbol){eps_1}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){error}<LSEP>[](symbol){eps_2}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){i}<LSEP>[](symbol){max_iter}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){break}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){candidate}<LEND>[call](){}<LSEP>[](symbol){ntrm_step}<LSEP>[](symbol){obj}<LSEP>[](symbol){delta}<LSEP>[](symbol){tau}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){p_x}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){fn}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){x}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){s}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){s}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){p_s}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){C}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){s}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){m0}<LEND>[call](){}<LSEP>[](symbol){ntrm_norm}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){r}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){kappa}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){kappa}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){acceptance}<LEND>[call](){}<LSEP>[](symbol){ntrm_reductions}<LSEP>[](symbol){obj}<LSEP>[](symbol){candidate}<LSEP>[](symbol){mu}<LSEP>[](symbol){nu}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){nu}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){acceptance}<LSEP>[](symbol){nu}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){acceptance}<LSEP>[](symbol){rho}<LEND>[](symbol){eta}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){obj}<LEND>[call](){}<LSEP>[](symbol){ntrm_update_solution}<LSEP>[](symbol){obj}<LSEP>[](symbol){candidate}<LSEP>[](symbol){gh}<LSEP>[](symbol){mu}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){acceptance}<LSEP>[](symbol){rho}<LEND>[argument 1; litteral](real){0.900000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){delta}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){delta}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){7.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){p_norm}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){acceptance}<LSEP>[](symbol){rho}<LEND>[argument 1; litteral](real){0.300000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){delta}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){delta}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){candidate}<LSEP>[](symbol){p_norm}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){delta}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){0.250000}<LSEP>[](symbol){delta}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){delta}<LSEP>[litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){nu}<LSEP>[litteral](real){0.500000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){mu}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){0.200000}<LSEP>[](symbol){mu}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){u}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){G}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){mu}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){m}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){ntrm_lagrange_multiplier}<LSEP>[](symbol){obj}<LSEP>[](symbol){mu}<LEND>[statement 24; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){obj}<LSEP>[](symbol){f}<LEND>[](symbol){converged}<LSEP>[](symbol){i}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){util.outflank.plotter}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){withOutliers}<LSEP>[](symbol){NoCorr}<LSEP>[](symbol){Hmin}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){Zoom}<LSEP>[](symbol){RightZoomFraction}<LSEP>[](symbol){titletext}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){results}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){results}<LEND>[](symbol){He}<LEND>[](symbol){Hmin}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){NoCorr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){FSTNoCorr}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){fbar}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){T1NoCorr}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){T2NoCorr}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){titletext}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){titletext}<LSEP>[argument 1; litteral](str){Fst without sample size correc...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){NoCorr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){FST}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){fbar}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){FSTbar}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){titletext}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){titletext}<LSEP>[argument 1; litteral](str){Fst with sample size correction}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){flist}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){flist}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){keeperlist}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){OutlierFlag}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){withOutliers}<LEND>[true branch; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){flist}<LSEP>[](symbol){keeperlist}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){Zoom}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){FstDistPlotterZoom}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){dfInferred}<LEND>[](symbol){flist}<LSEP>[](symbol){fbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){titletext}<LSEP>[](symbol){RightZoomFraction}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){FstDistPlotter}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){dfInferred}<LEND>[](symbol){flist}<LSEP>[](symbol){fbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){titletext}<LEND>[assign](){=}<LSEP>[](symbol){FstDistPlotter}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){df}<LSEP>[](symbol){FSTlist}<LSEP>[](symbol){FSTbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){titletext}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){xPlotUpperBound}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){FSTlist}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){breakslist}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xPlotUpperBound}<LSEP>[](symbol){binwidth}<LEND>[](symbol){binwidth}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){breaks}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){breakslist}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){x}<LSEP>[](symbol){breakslist}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){breaks}<LEND>[body; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){FSTlist}<LEND>[](symbol){y}<LEND>[statement 7; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){FSTlist}<LSEP>[argument 1; litteral](str){darkgoldenrod1}<LSEP>[](symbol){breakslist}<LSEP>[](symbol){F}<LSEP>[argument 4; litteral](str){Fst}<LSEP>[](symbol){titletext}<LEND>[statement 8; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[argument 2; litteral](str){darkblue}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[assign](){=}<LSEP>[](symbol){FstDistPlotterZoom}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){df}<LSEP>[](symbol){FSTlist}<LSEP>[](symbol){FSTbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){titletext}<LSEP>[](symbol){RightZoomFraction}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){FSTlistNoNA}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){FSTlist}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){FSTlist}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){xPlotUpperBound}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){FSTlistNoNA}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){xPlotLowerBound}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){quantile}<LSEP>[](symbol){FSTlistNoNA}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){RightZoomFraction}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){FSTlistNoNA}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){FSTlistNoNA}<LSEP>[](symbol){xPlotLowerBound}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){breakslist}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){xPlotLowerBound}<LSEP>[](symbol){xPlotUpperBound}<LSEP>[](symbol){binwidth}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){breaks}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){breakslist}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){x}<LSEP>[](symbol){breakslist}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 8; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){breaks}<LEND>[body; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xPlotLowerBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xPlotLowerBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){FSTlistNoNA}<LEND>[](symbol){y}<LEND>[statement 10; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){flist}<LSEP>[argument 1; litteral](str){darkgoldenrod1}<LSEP>[](symbol){breakslist}<LSEP>[](symbol){F}<LSEP>[argument 4; litteral](str){Fst}<LSEP>[](symbol){titletext}<LEND>[statement 11; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[argument 2; litteral](str){darkblue}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[assign](){=}<LSEP>[](symbol){FstDistPlotterAddBadCurve}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){df}<LSEP>[](symbol){FSTlist}<LSEP>[](symbol){FSTbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){RightZoomFraction}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){FSTlistNoNA}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){FSTlist}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){FSTlist}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){xPlotUpperBound}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){FSTlistNoNA}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){xPlotLowerBound}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){quantile}<LSEP>[](symbol){FSTlistNoNA}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){RightZoomFraction}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){breakslist}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){xPlotLowerBound}<LSEP>[](symbol){xPlotUpperBound}<LSEP>[](symbol){binwidth}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){breaks}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){breakslist}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){x}<LSEP>[](symbol){breakslist}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){breaks}<LEND>[body; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xPlotLowerBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){xPlotLowerBound}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.500000}<LEND>[](symbol){binwidth}<LEND>[](symbol){FSTbar}<LEND>[](symbol){df}<LEND>[](symbol){df}<LEND>[statement 8; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){FSTlistNoNA}<LEND>[](symbol){y}<LEND>[statement 9; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[argument 2; litteral](str){red}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[assign](){=}<LSEP>[](symbol){OutFLANKBadCurvePlotter}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){badDF}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){withOutliers}<LSEP>[](symbol){NoCorr}<LSEP>[](symbol){Hmin}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){Zoom}<LSEP>[](symbol){RightZoomFraction}<LSEP>[](symbol){titletext}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){results}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){results}<LEND>[](symbol){He}<LEND>[](symbol){Hmin}<LEND>[](symbol){}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){NoCorr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){FSTNoCorr}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){fbar}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){T1NoCorr}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){T2NoCorr}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){NoCorr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){FST}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){fbar}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){OFoutput}<LSEP>[](symbol){FSTbar}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){flist}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){flist}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){keeperlist}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){OutlierFlag}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){withOutliers}<LEND>[true branch; assign](){=}<LSEP>[](symbol){flist}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){flist}<LSEP>[](symbol){keeperlist}<LEND>[statement 6; call](){}<LSEP>[](symbol){FstDistPlotterAddBadCurve}<LSEP>[](symbol){badDF}<LSEP>[](symbol){flist}<LSEP>[](symbol){fbar}<LSEP>[](symbol){binwidth}<LSEP>[](symbol){RightZoomFraction}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.onLoad}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){libname}<LSEP>[](symbol){pkgname}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){op}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](str){default}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){toset}<LEND>[call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){op}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){options}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){toset}<LEND>[true branch; call](){}<LSEP>[](symbol){options}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){op}<LSEP>[](symbol){toset}<LEND>[statement 3; call](){}<LSEP>[](symbol){invisible}<LEND>[assign](){<-}<LSEP>[](symbol){namesOrLabels}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){label}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){attr}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](str){label}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[](symbol){i}<LEND>[assign](){<-}<LSEP>[](symbol){render.value}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){.default}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){suppressWarnings}<LEND>[argument 0; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[](symbol){.default}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){render.count}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){.default}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){suppressWarnings}<LEND>[argument 0; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[](symbol){.default}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){render.npct}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){pct}<LSEP>[](symbol){.default}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){suppressWarnings}<LEND>[argument 0; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[](symbol){.default}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){%d (%0.1f%%)}<LSEP>[](symbol){x}<LSEP>[](symbol){pct}<LEND>[assign](){<-}<LSEP>[](symbol){ttt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){ttt}<LEND>[assign](){<-}<LSEP>[](symbol){ttt.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){formula}<LSEP>[](symbol){...}<LSEP>[](symbol){render}<LSEP>[](symbol){lab}<LSEP>[](symbol){caption}<LSEP>[](symbol){footnote}<LSEP>[](symbol){expand.along}<LSEP>[](symbol){drop}<LSEP>[](symbol){collapse.cells}<LSEP>[](symbol){topclass}<LSEP>[](symbol){id}<LSEP>[](symbol){css}<LSEP>[](symbol){row.names}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){formula}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){value}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.list}<LEND>[argument 0; call](){}<LSEP>[](symbol){format}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){eg}<LEND>[call](){}<LSEP>[](symbol){expand.grid}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rowvars}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eg}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){colvars}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eg}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){lab}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){lab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){rowvars}<LEND>[litteral](str){ }<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){rowvars}<LEND>[](symbol){lab}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){lab}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){lab}<LSEP>[argument 1; litteral](str){.suppressrowlabels}<LEND>[call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){row.names}<LEND>[statement 7; call](){}<LSEP>[](symbol){ttt.numeric}<LSEP>[](symbol){value}<LSEP>[](symbol){rowvars}<LSEP>[](symbol){colvars}<LSEP>[](symbol){render}<LSEP>[](symbol){lab}<LSEP>[](symbol){caption}<LSEP>[](symbol){footnote}<LSEP>[](symbol){expand.along}<LSEP>[](symbol){drop}<LSEP>[](symbol){collapse.cells}<LSEP>[](symbol){topclass}<LSEP>[](symbol){id}<LSEP>[](symbol){css}<LSEP>[](symbol){...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){ttt.formula}<LSEP>[](symbol){formula}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LSEP>[](symbol){render}<LSEP>[](symbol){lab}<LSEP>[](symbol){caption}<LSEP>[](symbol){footnote}<LSEP>[](symbol){expand.along}<LSEP>[](symbol){drop}<LSEP>[](symbol){collapse.cells}<LSEP>[](symbol){topclass}<LSEP>[](symbol){id}<LSEP>[](symbol){css}<LEND>[assign](){<-}<LSEP>[](symbol){ttt.formula}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){data}<LSEP>[](symbol){...}<LSEP>[](symbol){render}<LSEP>[](symbol){lab}<LSEP>[](symbol){caption}<LSEP>[](symbol){footnote}<LSEP>[](symbol){expand.along}<LSEP>[](symbol){drop}<LSEP>[](symbol){collapse.cells}<LSEP>[](symbol){topclass}<LSEP>[](symbol){id}<LSEP>[](symbol){css}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dummy}<LSEP>[litteral](NULL){NULL}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dummy}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){data}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){1}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dummy}<LSEP>[argument 1; litteral](str){label}<LEND>[litteral](str){Count}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dummy}<LSEP>[argument 1; litteral](str){label}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[litteral](NULL){NULL}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){Formula}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){model.frame}<LSEP>[](symbol){f}<LSEP>[](symbol){data}<LSEP>[](symbol){na.pass}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){dummy}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){model.part}<LSEP>[](symbol){f}<LSEP>[](symbol){m}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xname}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LSEP>[](symbol){dummy}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xname}<LSEP>[litteral](str){dummy}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){rowvars}<LEND>[call](){}<LSEP>[](symbol){model.part}<LSEP>[](symbol){f}<LSEP>[](symbol){m}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){rowvars}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rowvars}<LSEP>[litteral](NULL){NULL}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){lab}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){lab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lab}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){lab}<LSEP>[argument 1; litteral](str){.suppressrowlabels}<LEND>[litteral](logical){TRUE}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){f}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){colvars}<LEND>[call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){model.part}<LSEP>[](symbol){f}<LSEP>[](symbol){m}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){colvars}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){xname}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){colvars}<LEND>[](symbol){xname}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; assign](){<-}<LSEP>[](symbol){xlabel}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){label}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){colvars}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){xlabel}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){lab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lab}<LSEP>[litteral](NULL){NULL}<LEND>[statement 8; call](){}<LSEP>[](symbol){ttt.numeric}<LSEP>[](symbol){x}<LSEP>[](symbol){rowvars}<LSEP>[](symbol){colvars}<LSEP>[](symbol){render}<LSEP>[](symbol){lab}<LSEP>[](symbol){caption}<LSEP>[](symbol){footnote}<LSEP>[](symbol){expand.along}<LSEP>[](symbol){drop}<LSEP>[](symbol){collapse.cells}<LSEP>[](symbol){topclass}<LSEP>[](symbol){id}<LSEP>[](symbol){css}<LSEP>[](symbol){...}<LEND>[assign](){<-}<LSEP>[](symbol){ttt.numeric}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){rowvars}<LSEP>[](symbol){colvars}<LSEP>[](symbol){...}<LSEP>[](symbol){render}<LSEP>[](symbol){lab}<LSEP>[](symbol){caption}<LSEP>[](symbol){footnote}<LSEP>[](symbol){expand.along}<LSEP>[](symbol){drop}<LSEP>[](symbol){collapse.cells}<LSEP>[](symbol){topclass}<LSEP>[](symbol){id}<LSEP>[](symbol){css}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){statslab}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){expand.along}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){statslab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){statslab}<LSEP>[litteral](str){Statistic}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){expand.along}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){expand.along}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tab}<LEND>[call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){rowvars}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){colvars}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){rowvars}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){colvars}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){rowvars}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){rowvars}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){counts}<LSEP>[](symbol){tab}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){counts}<LEND>[litteral](str){ftable}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){counts}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){counts}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){counts}<LSEP>[argument 1; litteral](str){row.vars}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){counts}<LSEP>[argument 1; litteral](str){col.vars}<LEND>[call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){tab}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){counts}<LEND>[call](){}<LSEP>[](symbol){ftable}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){rowvars}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){colvars}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){rowvars}<LEND>[argument 2; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){colvars}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){lab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lab}<LSEP>[litteral](NULL){NULL}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){render}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){counts}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){render}<LSEP>[](symbol){render.value}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){render}<LSEP>[](symbol){render.count}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){expand.along}<LSEP>[argument 1; litteral](str){rows}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){text}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){rowvars}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){colvars}<LEND>[](symbol){render}<LSEP>[](symbol){...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){text}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){split}<LEND>[argument 0; call](){}<LSEP>[](symbol){unname}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){colvars}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){rowvars}<LEND>[](symbol){render}<LSEP>[](symbol){...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){get.html.class}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](str){html.class}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){z}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){z}<LSEP>[litteral](str){}<LEND>[statement 2; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){html.class}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){text}<LSEP>[](symbol){get.html.class}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){stats}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){text}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){nstats}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){stats}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){text}<LEND>[call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){text}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){html.class}<LEND>[call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){html.class}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){expand.along}<LSEP>[argument 1; litteral](str){rows}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){text}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){text}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){counts}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){html.class}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[](symbol){html.class}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){counts}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){counts}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){row.vars}<LEND>[call](){}<LSEP>[](symbol){namesOrLabels}<LSEP>[](symbol){rowvars}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){col.vars}<LEND>[call](){}<LSEP>[](symbol){namesOrLabels}<LSEP>[](symbol){colvars}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nstats}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){expand.along}<LSEP>[argument 1; litteral](str){rows}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){counts}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){counts}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){counts}<LEND>[](symbol){nstats}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){row.vars}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){row.vars}<LEND>[argument 1; call](){}<LSEP>[](symbol){setNames}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){stats}<LEND>[](symbol){statslab}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){lab}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){lab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lab}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){lab}<LSEP>[argument 1; litteral](str){.suppressrowlabels}<LEND>[litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){counts}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){counts}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){counts}<LEND>[](symbol){nstats}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){col.vars}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){col.vars}<LEND>[argument 1; call](){}<LSEP>[](symbol){setNames}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){stats}<LEND>[](symbol){statslab}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){counts}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){text}<LEND>[litteral](real){0.000000}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){dim}<LEND>[call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){counts}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){counts}<LEND>[](symbol){a}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){text}<LEND>[](symbol){a}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){html.class}<LEND>[](symbol){a}<LEND>[statement 23; call](){}<LSEP>[](symbol){ttt.ftable}<LSEP>[](symbol){counts}<LSEP>[](symbol){text}<LSEP>[](symbol){lab}<LSEP>[](symbol){caption}<LSEP>[](symbol){footnote}<LSEP>[](symbol){drop}<LSEP>[](symbol){collapse.cells}<LSEP>[](symbol){html.class}<LSEP>[](symbol){topclass}<LSEP>[](symbol){id}<LSEP>[](symbol){css}<LEND>[assign](){<-}<LSEP>[](symbol){ttt.ftable}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){text}<LSEP>[](symbol){lab}<LSEP>[](symbol){caption}<LSEP>[](symbol){footnote}<LSEP>[](symbol){drop}<LSEP>[](symbol){collapse.cells}<LSEP>[](symbol){html.class}<LSEP>[](symbol){topclass}<LSEP>[](symbol){id}<LSEP>[](symbol){css}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){.ttt.ftable.internal}<LSEP>[](symbol){x}<LSEP>[](symbol){text}<LSEP>[](symbol){lab}<LSEP>[](symbol){caption}<LSEP>[](symbol){footnote}<LSEP>[](symbol){drop}<LSEP>[](symbol){collapse.cells}<LSEP>[](symbol){html.class}<LSEP>[](symbol){topclass}<LSEP>[](symbol){id}<LSEP>[](symbol){css}<LEND>[assign](){<-}<LSEP>[](symbol){.ttt.ftable.internal}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){text}<LSEP>[](symbol){lab}<LSEP>[](symbol){caption}<LSEP>[](symbol){footnote}<LSEP>[](symbol){drop}<LSEP>[](symbol){collapse.cells}<LSEP>[](symbol){html.class}<LSEP>[](symbol){topclass}<LSEP>[](symbol){id}<LSEP>[](symbol){css}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){ftable}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'x' must be an "ftable" object}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all.equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){text}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'x' and 'text' must be have th...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){html.class}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all.equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){html.class}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'x' and 'html.class' must be h...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){drop}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){drop}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){xrv}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){row.vars}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){xcv}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){col.vars}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){rlab}<LEND>[call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){expand.grid}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){xrv}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){clab}<LEND>[call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){expand.grid}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){xcv}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){zr}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){sum}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){zc}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sum}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){html.class}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){hcls}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[](symbol){prod}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){hcls}<LEND>[call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){hcls}<LSEP>[](symbol){html.class}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){drop}<LSEP>[argument 1; litteral](str){both}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){text}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){text}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zr}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zc}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){hcls}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hcls}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zr}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zc}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rlab}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rlab}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zr}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){clab}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clab}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zc}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){drop}<LSEP>[argument 1; litteral](str){rows}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){text}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){text}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zr}<LEND>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){hcls}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hcls}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zr}<LEND>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rlab}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rlab}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zr}<LEND>[](symbol){}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){drop}<LSEP>[argument 1; litteral](str){columns}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){text}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){text}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zc}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){hcls}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hcls}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zc}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){clab}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clab}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){zc}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){collapseLabels}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){lab}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){lab}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lab}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){z2}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lab}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){paste0}<LSEP>[argument 3; litteral](str){.}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){z}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){z}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){z2}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){z2}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LEND>[litteral](str){}<LEND>[](symbol){z}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){lab}<LEND>[](symbol){res}<LEND>[statement 13; control flow](){if}<LSEP>[](symbol){collapse.cells}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rlab}<LEND>[call](){}<LSEP>[](symbol){collapseLabels}<LSEP>[](symbol){rlab}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){clab}<LEND>[call](){}<LSEP>[](symbol){collapseLabels}<LSEP>[](symbol){clab}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){makeRowLabelTags}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rlab}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){rlab}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rlab}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ind}<LEND>[call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){z}<LSEP>[argument 1; litteral](str){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){cumsum}<LSEP>[](symbol){ind}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){sp}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){span}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ rowspan="%d"}<LSEP>[](symbol){span}<LEND>[argument 2; litteral](str){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ class="Rttt-rl Rttt-rl-lvl%d"}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){rlab}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){td}<LSEP>[litteral](str){td}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tags}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){<}<LSEP>[](symbol){td}<LSEP>[](symbol){sp}<LSEP>[](symbol){cl}<LSEP>[argument 4; litteral](str){>}<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){z}<LSEP>[](symbol){ind}<LEND>[argument 6; litteral](str){</}<LSEP>[](symbol){td}<LSEP>[argument 8; litteral](str){>\n}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){z}<LSEP>[](symbol){ind}<LEND>[](symbol){tags}<LEND>[](symbol){z}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){makeColLabelTags}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){clab}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){clab}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clab}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ind}<LEND>[call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){z}<LSEP>[argument 1; litteral](str){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){cumsum}<LSEP>[](symbol){ind}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){sp}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){span}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ colspan="%d"}<LSEP>[](symbol){span}<LEND>[argument 2; litteral](str){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ class="Rttt-cl Rttt-cl-lvl%d"}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){clab}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){td}<LSEP>[litteral](str){th}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tags}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){<}<LSEP>[](symbol){td}<LSEP>[](symbol){sp}<LSEP>[](symbol){cl}<LSEP>[argument 4; litteral](str){>}<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){z}<LSEP>[](symbol){ind}<LEND>[argument 6; litteral](str){</}<LSEP>[](symbol){td}<LSEP>[argument 8; litteral](str){>\n}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){z}<LSEP>[](symbol){ind}<LEND>[](symbol){tags}<LEND>[](symbol){z}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){rltags}<LEND>[call](){}<LSEP>[](symbol){makeRowLabelTags}<LSEP>[](symbol){rlab}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){cltags}<LEND>[call](){}<LSEP>[](symbol){makeColLabelTags}<LSEP>[](symbol){clab}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){makeRowLabelHeadTags}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rhlab}<LSEP>[](symbol){span}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sp}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){span}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ rowspan="%d"}<LSEP>[](symbol){span}<LEND>[false branch; litteral](str){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cl}<LSEP>[litteral](str){ class="Rttt-rlh"}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){td}<LSEP>[litteral](str){th}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tags}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){<}<LSEP>[](symbol){td}<LSEP>[](symbol){sp}<LSEP>[](symbol){cl}<LSEP>[argument 4; litteral](str){>}<LSEP>[](symbol){rhlab}<LSEP>[argument 6; litteral](str){</}<LSEP>[](symbol){td}<LSEP>[argument 8; litteral](str){>\n}<LEND>[](symbol){tags}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){.suppressrowlabels}<LSEP>[litteral](logical){FALSE}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){lab}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){lab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){.suppressrowlabels}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){lab}<LSEP>[argument 1; litteral](str){.suppressrowlabels}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){.suppressrowlabels}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){.suppressrowlabels}<LSEP>[litteral](logical){FALSE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lab}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){span}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){text}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sp}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){span}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ colspan="%d"}<LSEP>[](symbol){span}<LEND>[false branch; litteral](str){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cl}<LSEP>[litteral](str){ class="Rttt-lab"}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){td}<LSEP>[litteral](str){th}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){tags}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){<}<LSEP>[](symbol){td}<LSEP>[](symbol){sp}<LSEP>[](symbol){cl}<LSEP>[argument 4; litteral](str){>}<LSEP>[](symbol){lab}<LSEP>[argument 6; litteral](str){</}<LSEP>[](symbol){td}<LSEP>[argument 8; litteral](str){>\n}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){cltags}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){tags}<LSEP>[](symbol){cltags}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){rlhtags}<LEND>[call](){}<LSEP>[](symbol){makeRowLabelHeadTags}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){xrv}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cltags}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){thead}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){cltags}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tags}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cltags}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){.suppressrowlabels}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){rlhtags}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tags}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rlhtags}<LSEP>[](symbol){j}<LEND>[](symbol){tags}<LEND>[statement 2; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){<tr>\n}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){tags}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; litteral](str){</tr>\n}<LSEP>[argument 3; litteral](str){}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){text}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){ncolumns}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){dat}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){rltags}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){hcls}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){hcls}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){hcls}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){hcls}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){hcls}<LSEP>[argument 1; litteral](str){}<LEND>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){ class="}<LEND>[argument 1; call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){.}<LSEP>[argument 1; litteral](str){-}<LEND>[argument 2; call](){}<LSEP>[](symbol){make.names}<LSEP>[](symbol){hcls}<LEND>[argument 3; litteral](logical){TRUE}<LEND>[argument 2; litteral](str){"}<LEND>[statement 27; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){hcls}<LEND>[call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){dat}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){tbody}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){dat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){td}<LSEP>[litteral](str){td}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tags}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){<}<LSEP>[](symbol){td}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hcls}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 3; litteral](str){>}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dat}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 5; litteral](str){</}<LSEP>[](symbol){td}<LSEP>[argument 7; litteral](str){>\n}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){.suppressrowlabels}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){rltags}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tags}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){rltags}<LSEP>[](symbol){j}<LEND>[](symbol){i}<LEND>[](symbol){tags}<LEND>[statement 3; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){<tr>\n}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){tags}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; litteral](str){</tr>\n}<LSEP>[argument 3; litteral](str){}<LEND>[statement 29; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){caption}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){caption}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){caption}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){<caption>%s</caption>\n}<LSEP>[](symbol){caption}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){caption}<LSEP>[litteral](str){}<LEND>[statement 30; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){footnote}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){footnote}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){footnote}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){<p>%s</p>\n}<LSEP>[](symbol){footnote}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){footnote}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){footnote}<LSEP>[argument 1; litteral](str){\n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){tfoot}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){<tfoot><tr><td colspan="%d">...}<LSEP>[](symbol){ncolumns}<LSEP>[](symbol){footnote}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tfoot}<LSEP>[litteral](str){}<LEND>[statement 31; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){topclass}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){topclass}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){topclass}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ class="%s"}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){.}<LSEP>[argument 1; litteral](str){-}<LEND>[argument 2; call](){}<LSEP>[](symbol){make.names}<LSEP>[](symbol){topclass}<LEND>[argument 3; litteral](logical){TRUE}<LEND>[argument 2; litteral](str){ }<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){topclass}<LSEP>[litteral](str){}<LEND>[statement 32; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){id}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){id}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){id}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ id="%s"}<LEND>[argument 1; call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){.}<LSEP>[argument 1; litteral](str){-}<LEND>[argument 2; call](){}<LSEP>[](symbol){make.names}<LSEP>[](symbol){id}<LEND>[argument 3; litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){id}<LSEP>[litteral](str){}<LEND>[statement 33; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){css}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){css}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){css}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){<style type="text/css">%s</s...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){css}<LSEP>[argument 1; litteral](str){\n}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){css}<LSEP>[litteral](str){}<LEND>[statement 34; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){\n%s<table%s%s>\n%s<thead>\n}<LSEP>[](symbol){css}<LSEP>[](symbol){topclass}<LSEP>[](symbol){id}<LSEP>[](symbol){caption}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){thead}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){</thead>\n%s<tbody>\n}<LSEP>[](symbol){tfoot}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){tbody}<LSEP>[argument 1; litteral](str){}<LEND>[argument 4; litteral](str){</tbody>\n</table>\n}<LEND>[statement 35; call](){}<LSEP>[](symbol){structure}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){ttt}<LSEP>[argument 1; litteral](str){html}<LSEP>[argument 2; litteral](str){character}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[assign](){<-}<LSEP>[](symbol){print.ttt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LSEP>[](symbol){theme}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){theme}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){default}<LSEP>[argument 1; litteral](str){booktabs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){theme %s not supported; using ...}<LSEP>[](symbol){theme}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){theme}<LSEP>[litteral](str){default}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){interactive}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){htmltools}<LSEP>[](symbol){HTML}<LEND>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){style}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){htmltools}<LSEP>[](symbol){htmlDependency}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ttt_%s}<LSEP>[](symbol){theme}<LEND>[argument 1; litteral](str){1.0}<LEND>[argument 2; call](){}<LSEP>[](symbol){system.file}<LSEP>[argument 0; litteral](str){ttt}<LEND>[argument 1; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ttt_%s_1.0}<LSEP>[](symbol){theme}<LEND>[argument 3; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ttt_%s.css}<LSEP>[](symbol){theme}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){htmltools}<LSEP>[](symbol){div}<LEND>[argument 0; litteral](str){Rttt}<LSEP>[](symbol){style}<LSEP>[](symbol){z}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){htmltools}<LSEP>[](symbol){browsable}<LEND>[](symbol){z}<LEND>[statement 4; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){z}<LSEP>[](symbol){...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[](symbol){x}<LEND>[statement 2; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){knit_print.ttt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LSEP>[](symbol){theme}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){theme}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){default}<LSEP>[argument 1; litteral](str){booktabs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){theme %s not supported; using ...}<LSEP>[](symbol){theme}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){theme}<LSEP>[litteral](str){default}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){knit_to_html}<LEND>[call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){opts_knit}<LEND>[](symbol){get}<LEND>[argument 0; litteral](str){rmarkdown.pandoc.to}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){^html}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){opts_knit}<LEND>[](symbol){get}<LEND>[argument 0; litteral](str){rmarkdown.pandoc.to}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){knit_to_html}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){htmltools}<LSEP>[](symbol){HTML}<LEND>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){style}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){htmltools}<LSEP>[](symbol){htmlDependency}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ttt_%s}<LSEP>[](symbol){theme}<LEND>[argument 1; litteral](str){1.0}<LEND>[argument 2; call](){}<LSEP>[](symbol){system.file}<LSEP>[argument 0; litteral](str){ttt}<LEND>[argument 1; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ttt_%s_1.0}<LSEP>[](symbol){theme}<LEND>[argument 3; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){ttt_%s.css}<LSEP>[](symbol){theme}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){htmltools}<LSEP>[](symbol){div}<LEND>[argument 0; litteral](str){Rttt}<LSEP>[](symbol){style}<LSEP>[](symbol){z}<LEND>[statement 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){knit_print}<LEND>[](symbol){z}<LSEP>[](symbol){...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){knitr}<LSEP>[](symbol){knit_print}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){x}<LEND>[](symbol){...}

[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){print.ada}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){kapstat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tab}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){tab}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){tab}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){tab}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rs}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){tab}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){sum}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cs}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){tab}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){sum}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){N}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){rs}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){E}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){rs}<LSEP>[](symbol){cs}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){N}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){O}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){tab}<LEND>[](symbol){N}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){O}<LSEP>[](symbol){E}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){E}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](logical){NA}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){call}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cl}<LEND>[argument 1; litteral](real){2.000000}<LEND>[litteral](str){}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Call:\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){dput}<LSEP>[](symbol){cl}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){fit}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){tab}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){confusion}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){errm}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){tab}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){actual}<LEND>[statement 5; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nLoss:}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){model}<LEND>[](symbol){lossObj}<LEND>[](symbol){loss}<LEND>[argument 2; litteral](str){Method:}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){model}<LEND>[](symbol){lossObj}<LEND>[](symbol){type}<LEND>[argument 4; litteral](str){ Iteration:}<LEND>[argument 5; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){iter}<LEND>[argument 6; litteral](str){\n}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nFinal Confusion Matrix for D...}<LEND>[statement 7; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){tab}<LEND>[statement 8; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nTrain Error:}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){errm}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){iter}<LEND>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){which.min}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){model}<LEND>[](symbol){oob.str}<LEND>[](symbol){oobm.err}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){which.min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){model}<LEND>[](symbol){oob.str}<LEND>[](symbol){oobm.err}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 1; litteral](real){5.000000}<LEND>[statement 10; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nOut-Of-Bag Error: }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){model}<LEND>[](symbol){oob.str}<LEND>[](symbol){oobm.err}<LEND>[](symbol){j}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; litteral](str){ iteration=}<LSEP>[](symbol){j}<LSEP>[argument 4; litteral](str){\n}<LEND>[statement 11; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nAdditional Estimates of numb...}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){errs}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){model}<LEND>[](symbol){errs}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){errs}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){errs}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){errs}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){k}<LEND>[argument 2; litteral](str){}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){est.m}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){errs}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){which.min}<LEND>[statement 16; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){est.m}<LEND>[statement 17; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 18; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){print.foldermtg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LSEP>[](symbol){description}<LSEP>[](symbol){features}<LSEP>[](symbol){topology}<LSEP>[](symbol){coordinates}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){which.print}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){mtg.header}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){classes}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){which.print}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){which.print}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){classes}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){description}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){which.print}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){which.print}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){description}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){features}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){which.print}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){which.print}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){features}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){topology}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){which.print}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){which.print}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){topology}<LEND>[statement 5; control flow](){if}<LSEP>[](symbol){coordinates}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){which.print}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){which.print}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){coordinates}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){which.print}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){which.print}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){classes}<LSEP>[argument 1; litteral](str){description}<LSEP>[argument 2; litteral](str){features}<LSEP>[argument 3; litteral](str){topology}<LSEP>[argument 4; litteral](str){coordinates}<LEND>[statement 7; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){which.print}<LEND>[](symbol){...}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.compliance.check}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: genlight object...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SNP}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){scores}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](logical){NA}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Checking coding of SNPs\n}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){mat}<LEND>[](symbol){scores}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ SNP data scored NA, 0, 1 o...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Error: SNP data must be sc...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){scores}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](logical){NA}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Checking coding of Tag P/A d...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){mat}<LEND>[](symbol){scores}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Tag P/A data (SilicoDArT) ...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Error: Tag P/A data (Silic...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Checking locus metrics and f...}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){utils.reset.flags}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Recalculating locus metrics\n}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.recalc.metrics}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Checking for monomorphic loci\n}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){gl.filter.monomorphs}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x2}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No monomorphic loci detect...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Dataset containes monomorp...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[litteral](logical){FALSE}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ The number of rows in the lo...}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Checking for individual metr...}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Creating a slot for indivi...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[](symbol){id}<LEND>[call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Individual metrics confirm...}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Checking for population assi...}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Population assignments not d...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](str){pop1}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Population assignments confi...}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlon}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlong}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlon}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlong}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlong}<LEND>[](symbol){long}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlong}<LEND>[](symbol){lon}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlong}<LEND>[](symbol){long}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlon}<LEND>[litteral](NULL){NULL}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlong}<LEND>[](symbol){long}<LEND>[litteral](NULL){NULL}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Spelling of coordinates checke...}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 28; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matddhellinger}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){x must be an object of class '...}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[body; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){ddhellinger}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){j}<LEND>[statement 4; call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){distances}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rt_ticket_attachment}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){ticket_id}<LSEP>[](symbol){attachment_id}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){url}<LEND>[call](){}<LSEP>[](symbol){rt_url}<LSEP>[argument 0; litteral](str){ticket}<LSEP>[](symbol){ticket_id}<LSEP>[argument 2; litteral](str){attachments}<LSEP>[](symbol){attachment_id}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){response}<LEND>[call](){}<LSEP>[](symbol){rt_GET}<LSEP>[](symbol){url}<LSEP>[](symbol){...}<LEND>[statement 2; call](){}<LSEP>[](symbol){stopforstatus}<LSEP>[](symbol){response}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){Ticket \\d+ does not exist}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){^Invalid attachment id:}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[](symbol){response}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.fixed.diff}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){tloc}<LSEP>[](symbol){test}<LSEP>[](symbol){delta}<LSEP>[](symbol){alpha}<LSEP>[](symbol){reps}<LSEP>[](symbol){mono.rm}<LSEP>[](symbol){pb}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){fd}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){fd}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){gl}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ fd object detected\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight or fd ob...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){tloc}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){tloc}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Parameter tloc sh...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){tloc}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Comparing populations for fi...}<LSEP>[](symbol){tloc}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){tloc}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Comparing populations for ab...}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Distance calculat...}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Monomorphic loci reta...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Monomorphic loci removed\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.filter.monomorphs}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){ftable}<LEND>[call](){}<LSEP>[](symbol){gl.percent.freq}<LSEP>[](symbol){x}<LSEP>[](symbol){verbose}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Populations, aggregations and ...}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Fixed differences can...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Some sample sizes are small ...}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){)\n}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){test}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Recommend manually amalgamat...}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){npops}<LEND>[call](){}<LSEP>[](symbol){nlevels}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ftable}<LSEP>[](symbol){popn}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){nloci}<LEND>[call](){}<LSEP>[](symbol){nlevels}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ftable}<LSEP>[](symbol){locus}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){fixed.matrix}<LEND>[call](){}<LSEP>[](symbol){array}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){exp.matrix}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){sd.matrix}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){pcfixed.matrix}<LEND>[call](){}<LSEP>[](symbol){array}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){ind.count.matrix}<LEND>[call](){}<LSEP>[](symbol){array}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){loc.count.matrix}<LEND>[call](){}<LSEP>[](symbol){array}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){p.false.pos.matrix}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){pb}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){progress}<LEND>[call](){}<LSEP>[](symbol){txtProgressBar}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](real){0.000000}<LSEP>[argument 4; litteral](str){Working ....}<LEND>[statement 1; call](){}<LSEP>[](symbol){getTxtProgressBar}<LSEP>[](symbol){progress}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Comparing populations pairwise...}<LEND>[statement 26; control flow](){for}<LSEP>[](symbol){popi}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){npops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){popj}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){popi}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){npops}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ftable}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ftable}<LSEP>[](symbol){popn}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[](symbol){popi}<LEND>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){p2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ftable}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ftable}<LSEP>[](symbol){popn}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[](symbol){popj}<LEND>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){fixed}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){nloci}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nloci}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixed}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){is.fixed}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p1}<LSEP>[](symbol){frequency}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p2}<LSEP>[](symbol){frequency}<LEND>[](symbol){i}<LEND>[](symbol){tloc}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixed.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){fixed}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loc.count.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){fixed}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pcfixed.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixed.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){fixed}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ind.count.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p1}<LSEP>[](symbol){nobs}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p1}<LSEP>[](symbol){nobs}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p2}<LSEP>[](symbol){nobs}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p2}<LSEP>[](symbol){nobs}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixed.matrix}<LSEP>[](symbol){popj}<LSEP>[](symbol){popi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixed.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixed.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popi}<LEND>[litteral](real){0.000000}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixed.matrix}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[litteral](real){0.000000}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){fixed.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){fixed.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loc.count.matrix}<LSEP>[](symbol){popj}<LSEP>[](symbol){popi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loc.count.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loc.count.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popi}<LEND>[litteral](logical){NA}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loc.count.matrix}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[litteral](logical){NA}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){loc.count.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){loc.count.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pcfixed.matrix}<LSEP>[](symbol){popj}<LSEP>[](symbol){popi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pcfixed.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pcfixed.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popi}<LEND>[litteral](real){0.000000}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pcfixed.matrix}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[litteral](real){0.000000}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){pcfixed.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){pcfixed.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ind.count.matrix}<LSEP>[](symbol){popj}<LSEP>[](symbol){popi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ind.count.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[statement 24; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ind.count.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popi}<LEND>[litteral](logical){NA}<LEND>[statement 25; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ind.count.matrix}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[litteral](logical){NA}<LEND>[statement 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){ind.count.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 27; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){ind.count.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 28; control flow](){if}<LSEP>[](symbol){test}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outlist}<LEND>[call](){}<LSEP>[](symbol){gl.utils.fdsim}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[](symbol){popi}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[](symbol){popj}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fixed.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[](symbol){delta}<LSEP>[](symbol){reps}<LSEP>[argument 5; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.false.pos.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outlist}<LSEP>[](symbol){prob}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exp.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outlist}<LSEP>[](symbol){mnexpected}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sd.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){outlist}<LSEP>[](symbol){sdexpected}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.false.pos.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[](symbol){alpha}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[](symbol){popi}<LEND>[argument 2; litteral](str){vs}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[](symbol){popj}<LEND>[argument 4; litteral](str){ [p =}<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.false.pos.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[argument 6; litteral](str){,ns]\n}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exp.matrix}<LSEP>[](symbol){popj}<LSEP>[](symbol){popi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exp.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exp.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popi}<LEND>[litteral](real){0.000000}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exp.matrix}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[litteral](real){0.000000}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){exp.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){exp.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sd.matrix}<LSEP>[](symbol){popj}<LSEP>[](symbol){popi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sd.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sd.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popi}<LEND>[litteral](real){0.000000}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sd.matrix}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[litteral](real){0.000000}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){sd.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){sd.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.false.pos.matrix}<LSEP>[](symbol){popj}<LSEP>[](symbol){popi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.false.pos.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popj}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.false.pos.matrix}<LSEP>[](symbol){popi}<LSEP>[](symbol){popi}<LEND>[litteral](real){0.000000}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.false.pos.matrix}<LSEP>[](symbol){npops}<LSEP>[](symbol){npops}<LEND>[litteral](real){0.000000}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){p.false.pos.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){p.false.pos.matrix}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){pb}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){progress}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){popi}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){npops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){pb}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Returning a list containing th...}<LSEP>[argument 1; litteral](str){ [[1]] $gl -- input ge...}<LSEP>[argument 2; litteral](str){ [[2]] $fd -- raw fixe...}<LSEP>[argument 3; litteral](str){ [[3]] $pcfd -- percen...}<LSEP>[argument 4; litteral](str){ [[4]] $nobs -- mean n...}<LSEP>[argument 5; litteral](str){ [[5]] $nloc -- total ...}<LSEP>[argument 6; litteral](str){ [[6]] $expfpos -- if ...}<LSEP>[argument 7; litteral](str){ [[7]] $sdfpos -- if t...}<LSEP>[argument 8; litteral](str){ [[8]] $prob -- if tes...}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){x}<LSEP>[](symbol){fixed.matrix}<LSEP>[](symbol){pcfixed.matrix}<LSEP>[](symbol){ind.count.matrix}<LSEP>[](symbol){loc.count.matrix}<LSEP>[](symbol){exp.matrix}<LSEP>[](symbol){sd.matrix}<LSEP>[](symbol){p.false.pos.matrix}<LEND>[statement 29; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){l}<LEND>[litteral](str){fd}<LEND>[statement 30; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 31; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){l}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){countPaths}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){d}<LSEP>[](symbol){debug}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){N}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){N}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){M}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){M}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){N}<LSEP>[](symbol){M}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){openBegin}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){}<LEND>[litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){dir}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){stepPattern}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){npats}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dir}<LSEP>[argument 1; litteral](str){npat}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){nsteps}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){dir}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){deltas}<LEND>[call](){}<LSEP>[](symbol){.mkDirDeltas}<LSEP>[](symbol){dir}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){wf}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){windowFunction}<LEND>[statement 9; control flow](){for}<LSEP>[](symbol){ii}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){N}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){jj}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.finite}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){ii}<LSEP>[](symbol){jj}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){next}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){do.call}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){windowFunction}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){ii}<LSEP>[](symbol){jj}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){call}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){ii}<LSEP>[](symbol){jj}<LEND>[litteral](real){0.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){next}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){np}<LSEP>[litteral](real){0.000000}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){npats}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ni}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ii}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deltas}<LSEP>[](symbol){k}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nj}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){jj}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deltas}<LSEP>[](symbol){k}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){ni}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){nj}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){np}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){np}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){ni}<LSEP>[](symbol){nj}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){ii}<LSEP>[](symbol){jj}<LEND>[](symbol){np}<LEND>[statement 10; control flow](){if}<LSEP>[](symbol){debug}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){m}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){openEnd}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){N}<LSEP>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){N}<LSEP>[](symbol){M}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rt_login}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){user}<LSEP>[](symbol){password}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){user}<LSEP>[argument 1; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){password}<LSEP>[argument 1; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[](symbol){interactive}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){rt_login_interactive}<LSEP>[](symbol){...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){rt_do_login}<LSEP>[](symbol){user}<LSEP>[](symbol){password}<LEND>[assign](){<-}<LSEP>[](symbol){rt_do_login}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){user}<LSEP>[](symbol){password}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){url}<LEND>[call](){}<LSEP>[](symbol){rt_url}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){response}<LEND>[call](){}<LSEP>[](symbol){rt_POST}<LSEP>[](symbol){url}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){user}<LSEP>[](symbol){password}<LEND>[argument 2; litteral](str){form}<LSEP>[](symbol){...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){check_login}<LSEP>[](symbol){response}<LEND>[statement 3; call](){}<LSEP>[](symbol){stopforstatus}<LSEP>[](symbol){response}<LEND>[statement 4; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){result}<LEND>[assign](){<-}<LSEP>[](symbol){check_login}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){response}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[argument 1; litteral](str){Invalid object specification: ...}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Login failed: }<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){message}<LEND>[argument 2; litteral](str){ (}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[argument 4; litteral](str){)}<LSEP>[argument 5; litteral](logical){FALSE}<LEND>[statement 1; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Successfully logged in.}<LEND>[statement 2; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[assign](){<-}<LSEP>[](symbol){rt_login_interactive}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rt_base_url}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){requireNamespace}<LSEP>[argument 0; litteral](str){askpass}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){The 'askpass' is required when...}<LSEP>[argument 1; litteral](str){Install it with install.packag...}<LSEP>[argument 2; litteral](str){\nYou can also set your passwo...}<LSEP>[argument 3; litteral](str){Sys.getenv(RT_PASSWORD="your ...}<LSEP>[argument 4; litteral](str){See ?rt for more details.}<LEND>[statement 1; call](){}<LSEP>[](symbol){rt_do_login}<LEND>[argument 0; call](){}<LSEP>[](symbol){trimws}<LEND>[argument 0; call](){}<LSEP>[](symbol){readline}<LSEP>[argument 0; litteral](str){Enter username: }<LEND>[argument 1; call](){}<LSEP>[](symbol){trimws}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){askpass}<LSEP>[](symbol){askpass}<LEND>[](symbol){rt_base_url}<LSEP>[](symbol){...}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.pkgenv}<LEND>[call](){}<LSEP>[](symbol){new.env}<LEND>[argument 0; call](){}<LSEP>[](symbol){emptyenv}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){units}<LEND>[litteral](str){inches}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){exportUnits}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){units}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){exportPPI}<LEND>[litteral](real){150.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){arrowAngle}<LEND>[litteral](real){30.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){arrowLength}<LEND>[litteral](real){0.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){arrowUnits}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){units}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){arrowEnds}<LEND>[litteral](str){last}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){arrowType}<LEND>[litteral](str){open}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){boxWidth}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){boxHeight}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){boxRadius}<LEND>[litteral](real){0.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){boxFillColor}<LEND>[litteral](str){transparent}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){boxOpacity}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){boxLineWidth}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){boxLineType}<LEND>[litteral](str){solid}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){boxLineColor}<LEND>[litteral](str){black}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){circleRadius}<LEND>[litteral](real){0.500000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){circleFillColor}<LEND>[litteral](str){transparent}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){circleOpacity}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){circleLineWidth}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){circleLineType}<LEND>[litteral](str){solid}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){circleLineColor}<LEND>[litteral](str){black}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curveCurvature}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curveAngle}<LEND>[litteral](real){90.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curvePoints}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curveShape}<LEND>[litteral](real){0.500000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curveSquare}<LEND>[litteral](logical){TRUE}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curveSquareShape}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curveOpacity}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curveLineColor}<LEND>[litteral](str){black}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curveLineWidth}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curveLineType}<LEND>[litteral](str){solid}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curveInflect}<LEND>[litteral](logical){FALSE}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){curveOpen}<LEND>[litteral](logical){TRUE}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){lineOpacity}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){lineWidth}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){lineType}<LEND>[litteral](str){solid}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){lineColor}<LEND>[litteral](str){black}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){pageWidth}<LEND>[litteral](real){8.500000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){pageHeight}<LEND>[litteral](real){11.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){pointPCH}<LEND>[litteral](real){20.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){pointSize}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){pointFillColor}<LEND>[litteral](str){transparent}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){pointOpacity}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){pointLineColor}<LEND>[litteral](str){black}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){pointLineType}<LEND>[litteral](str){solid}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){pointLineWidth}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){text}<LEND>[litteral](str){text}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){textJust}<LEND>[litteral](str){centre}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){textHjust}<LEND>[litteral](NULL){NULL}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){textVjust}<LEND>[litteral](NULL){NULL}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){textAngle}<LEND>[litteral](real){0.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){textOverlap}<LEND>[litteral](logical){FALSE}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){textOpacity}<LEND>[litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){textColor}<LEND>[litteral](str){black}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){textSize}<LEND>[litteral](real){12.000000}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){textFace}<LEND>[litteral](str){plain}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){textFamily}<LEND>[litteral](str){sans}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){textLineHeight}<LEND>[litteral](real){1.200000}<LEND>[assign](){<-}<LSEP>[](symbol){drawBox}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){width}<LSEP>[](symbol){height}<LSEP>[](symbol){radius}<LSEP>[](symbol){fillColor}<LSEP>[](symbol){opacity}<LSEP>[](symbol){lineColor}<LSEP>[](symbol){lineWidth}<LSEP>[](symbol){lineType}<LSEP>[](symbol){units}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){grid.roundrect}<LEND>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){width}<LSEP>[](symbol){height}<LEND>[argument 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){unit}<LEND>[](symbol){radius}<LSEP>[](symbol){units}<LEND>[argument 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){gpar}<LEND>[](symbol){fillColor}<LSEP>[](symbol){opacity}<LSEP>[](symbol){lineColor}<LSEP>[](symbol){lineWidth}<LSEP>[](symbol){lineType}<LEND>[](symbol){units}<LSEP>[](symbol){...}<LEND>[statement 1; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){out}<LEND>[assign](){<-}<LSEP>[](symbol){drawCircle}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){radius}<LSEP>[](symbol){fillColor}<LSEP>[](symbol){opacity}<LSEP>[](symbol){lineColor}<LSEP>[](symbol){lineWidth}<LSEP>[](symbol){lineType}<LSEP>[](symbol){units}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){grid.circle}<LEND>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){radius}<LEND>[argument 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){gpar}<LEND>[](symbol){fillColor}<LSEP>[](symbol){opacity}<LSEP>[](symbol){lineColor}<LSEP>[](symbol){lineWidth}<LSEP>[](symbol){lineType}<LEND>[](symbol){units}<LSEP>[](symbol){...}<LEND>[statement 1; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){out}<LEND>[assign](){<-}<LSEP>[](symbol){drawCurve}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){curvature}<LSEP>[](symbol){angle}<LSEP>[](symbol){points}<LSEP>[](symbol){shape}<LSEP>[](symbol){square}<LSEP>[](symbol){squareShape}<LSEP>[](symbol){opacity}<LSEP>[](symbol){lineColor}<LSEP>[](symbol){lineWidth}<LSEP>[](symbol){lineType}<LSEP>[](symbol){inflect}<LSEP>[](symbol){open}<LSEP>[](symbol){arrowAngle}<LSEP>[](symbol){arrowLength}<LSEP>[](symbol){arrowUnits}<LSEP>[](symbol){arrowEnds}<LSEP>[](symbol){arrowType}<LSEP>[](symbol){units}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){grid.curve}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){curvature}<LSEP>[](symbol){angle}<LSEP>[](symbol){points}<LSEP>[](symbol){shape}<LSEP>[](symbol){square}<LSEP>[](symbol){squareShape}<LSEP>[](symbol){inflect}<LSEP>[](symbol){open}<LEND>[argument 12; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){gpar}<LEND>[](symbol){opacity}<LSEP>[](symbol){lineColor}<LSEP>[](symbol){lineWidth}<LSEP>[](symbol){lineType}<LEND>[argument 13; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){arrow}<LEND>[](symbol){arrowAngle}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){unit}<LEND>[](symbol){arrowLength}<LSEP>[](symbol){arrowUnits}<LEND>[](symbol){arrowEnds}<LSEP>[](symbol){arrowType}<LEND>[](symbol){units}<LSEP>[](symbol){...}<LEND>[statement 1; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){out}<LEND>[assign](){<-}<LSEP>[](symbol){drawExport}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){f}<LSEP>[](symbol){width}<LSEP>[](symbol){height}<LSEP>[](symbol){ppi}<LSEP>[](symbol){format}<LSEP>[](symbol){textSize}<LSEP>[](symbol){units}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){format}<LEND>[call](){}<LSEP>[](symbol){tolower}<LSEP>[](symbol){format}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){supportedVectors}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){pdf}<LSEP>[argument 1; litteral](str){svg}<LSEP>[argument 2; litteral](str){eps}<LSEP>[argument 3; litteral](str){ps}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){supportedRasters}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){bmp}<LSEP>[argument 1; litteral](str){jpeg}<LSEP>[argument 2; litteral](str){jpg}<LSEP>[argument 3; litteral](str){png}<LSEP>[argument 4; litteral](str){tiff}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){units}<LEND>[call](){}<LSEP>[](symbol){tolower}<LSEP>[](symbol){units}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){supportedUnits}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){in}<LSEP>[argument 1; litteral](str){inches}<LSEP>[argument 2; litteral](str){inch}<LSEP>[argument 3; litteral](str){cm}<LSEP>[argument 4; litteral](str){centimeter}<LSEP>[argument 5; litteral](str){centimeters}<LSEP>[argument 6; litteral](str){centimetres}<LSEP>[argument 7; litteral](str){centimetre}<LSEP>[argument 8; litteral](str){px}<LSEP>[argument 9; litteral](str){pixel}<LSEP>[argument 10; litteral](str){pixels}<LSEP>[argument 11; litteral](str){pix}<LSEP>[argument 12; litteral](str){mm}<LSEP>[argument 13; litteral](str){millimeter}<LSEP>[argument 14; litteral](str){millimeters}<LSEP>[argument 15; litteral](str){millimetre}<LSEP>[argument 16; litteral](str){millimetres}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){units}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){inches}<LSEP>[argument 1; litteral](str){inch}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){units}<LSEP>[litteral](str){in}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){units}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){centimeter}<LSEP>[argument 1; litteral](str){centimeters}<LSEP>[argument 2; litteral](str){centimetres}<LSEP>[argument 3; litteral](str){centimetre}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){units}<LSEP>[litteral](str){cm}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){units}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){pixel}<LSEP>[argument 1; litteral](str){pixels}<LSEP>[argument 2; litteral](str){pix}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){units}<LSEP>[litteral](str){px}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){units}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){millimeter}<LSEP>[argument 1; litteral](str){millimeters}<LSEP>[argument 2; litteral](str){millimetre}<LSEP>[argument 3; litteral](str){millimetres}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){units}<LSEP>[litteral](str){mm}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){units}<LSEP>[](symbol){supportedUnits}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){msg}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Unknown unit }<LSEP>[argument 1; litteral](str){".}<LSEP>[](symbol){format}<LSEP>[argument 3; litteral](str){"}<LSEP>[argument 4; litteral](str){ for export. Supported units are:}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){supportedFormat}<LSEP>[](symbol){supportedUnits}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){msg}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){msg}<LSEP>[argument 1; litteral](str){\n *.}<LSEP>[](symbol){supportedFormat}<LEND>[statement 2; call](){}<LSEP>[](symbol){stop}<LSEP>[](symbol){msg}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){format}<LSEP>[](symbol){supportedVectors}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){format}<LSEP>[argument 1; litteral](str){ps}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){setPS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ps}<LEND>[call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){postscript}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){format}<LSEP>[argument 1; litteral](str){eps}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){setEPS}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){eps}<LEND>[call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){postscript}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){dev.copy}<LEND>[](symbol){pdf}<LSEP>[](symbol){f}<LSEP>[](symbol){width}<LSEP>[](symbol){height}<LSEP>[](symbol){textSize}<LSEP>[](symbol){...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){format}<LSEP>[](symbol){supportedRasters}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){jpg}<LEND>[call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){jpeg}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){dev.copy}<LEND>[argument 0; call](){}<LSEP>[](symbol){get}<LSEP>[](symbol){format}<LEND>[](symbol){f}<LSEP>[](symbol){width}<LSEP>[](symbol){height}<LSEP>[](symbol){units}<LSEP>[](symbol){textSize}<LSEP>[](symbol){ppi}<LSEP>[](symbol){...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){msg}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Unknown file format }<LSEP>[argument 1; litteral](str){".}<LSEP>[](symbol){format}<LSEP>[argument 3; litteral](str){"}<LSEP>[argument 4; litteral](str){ for export. Supported file fo...}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){supportedFormat}<LEND>[range; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){supportedVectors}<LSEP>[](symbol){supportedRasters}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){msg}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){msg}<LSEP>[argument 1; litteral](str){\n *.}<LSEP>[](symbol){supportedFormat}<LEND>[statement 2; call](){}<LSEP>[](symbol){stop}<LSEP>[](symbol){msg}<LEND>[statement 8; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){dev.off}<LEND>[statement 9; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){out}<LEND>[assign](){<-}<LSEP>[](symbol){drawLine}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){opacity}<LSEP>[](symbol){lineColor}<LSEP>[](symbol){lineWidth}<LSEP>[](symbol){lineType}<LSEP>[](symbol){arrowAngle}<LSEP>[](symbol){arrowLength}<LSEP>[](symbol){arrowUnits}<LSEP>[](symbol){arrowEnds}<LSEP>[](symbol){arrowType}<LSEP>[](symbol){units}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){grid.lines}<LEND>[](symbol){x}<LSEP>[](symbol){y}<LEND>[argument 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){gpar}<LEND>[](symbol){opacity}<LSEP>[](symbol){lineColor}<LSEP>[](symbol){lineWidth}<LSEP>[](symbol){lineType}<LEND>[argument 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){arrow}<LEND>[](symbol){arrowAngle}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){unit}<LEND>[](symbol){arrowLength}<LSEP>[](symbol){arrowUnits}<LEND>[](symbol){arrowEnds}<LSEP>[](symbol){arrowType}<LEND>[](symbol){units}<LSEP>[](symbol){...}<LEND>[statement 1; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){out}<LEND>[assign](){<-}<LSEP>[](symbol){drawPage}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){width}<LSEP>[](symbol){height}<LSEP>[](symbol){units}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){grid.newpage}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){units}<LEND>[](symbol){units}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){viewport}<LEND>[](symbol){width}<LSEP>[](symbol){height}<LSEP>[](symbol){units}<LSEP>[](symbol){...}<LEND>[statement 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){pushViewport}<LEND>[](symbol){out}<LEND>[statement 4; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){out}<LEND>[assign](){<-}<LSEP>[](symbol){drawPoint}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){pch}<LSEP>[](symbol){size}<LSEP>[](symbol){fillColor}<LSEP>[](symbol){opacity}<LSEP>[](symbol){lineColor}<LSEP>[](symbol){lineWidth}<LSEP>[](symbol){lineType}<LSEP>[](symbol){units}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){grid.points}<LEND>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){pch}<LEND>[argument 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){unit}<LEND>[](symbol){size}<LSEP>[](symbol){units}<LEND>[argument 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){gpar}<LEND>[](symbol){fillColor}<LSEP>[](symbol){opacity}<LSEP>[](symbol){lineColor}<LSEP>[](symbol){lineWidth}<LSEP>[](symbol){lineType}<LEND>[](symbol){units}<LEND>[statement 1; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){out}<LEND>[assign](){<-}<LSEP>[](symbol){drawSettings}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){settings}<LEND>[call](){}<LSEP>[](symbol){as.list}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){keys}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){settings}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){s}<LEND>[range; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){keys}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){keys}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){.pkgenv}<LSEP>[](symbol){s}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){settings}<LSEP>[](symbol){s}<LEND>[statement 3; call](){}<LSEP>[](symbol){invisible}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.list}<LSEP>[](symbol){.pkgenv}<LEND>[assign](){<-}<LSEP>[](symbol){drawText}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){text}<LSEP>[](symbol){just}<LSEP>[](symbol){hjust}<LSEP>[](symbol){vjust}<LSEP>[](symbol){angle}<LSEP>[](symbol){overlap}<LSEP>[](symbol){opacity}<LSEP>[](symbol){color}<LSEP>[](symbol){size}<LSEP>[](symbol){face}<LSEP>[](symbol){family}<LSEP>[](symbol){lineHeight}<LSEP>[](symbol){units}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){grid.text}<LEND>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){text}<LSEP>[](symbol){just}<LSEP>[](symbol){hjust}<LSEP>[](symbol){vjust}<LSEP>[](symbol){angle}<LSEP>[](symbol){overlap}<LEND>[argument 8; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){gpar}<LEND>[](symbol){opacity}<LSEP>[](symbol){color}<LSEP>[](symbol){size}<LSEP>[](symbol){face}<LSEP>[](symbol){family}<LSEP>[](symbol){lineHeight}<LEND>[](symbol){units}<LEND>[statement 1; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){out}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){is.folderh}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){folderh}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){print.RD}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nCall:\n}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){call}<LEND>[argument 1; litteral](str){\n}<LSEP>[argument 2; litteral](str){\n}<LEND>[argument 2; litteral](str){\n\n}<LSEP>[argument 3; litteral](str){}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Coefficients:\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print.default}<LEND>[argument 0; call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){est}<LEND>[](symbol){digits}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 4; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){util.outflank}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){FstDataFrame}<LSEP>[](symbol){LeftTrimFraction}<LSEP>[](symbol){RightTrimFraction}<LSEP>[](symbol){Hmin}<LSEP>[](symbol){NumberOfSamples}<LSEP>[](symbol){qthreshold}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){Fstdata}<LEND>[call](){}<LSEP>[](symbol){outputDFStarterNoCorr}<LSEP>[](symbol){FstDataFrame}<LSEP>[](symbol){Hmin}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){workingDataFrame}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Fstdata}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){Fstdata}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){storedDataFrameNA}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Fstdata}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){Fstdata}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){sortedDataFrame}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){workingDataFrame}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){NLociTotal}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sortedDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){SmallestKeeper}<LEND>[call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){NLociTotal}<LSEP>[](symbol){LeftTrimFraction}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){LargestKeeper}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){NLociTotal}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){RightTrimFraction}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){LowTrimPoint}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sortedDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){SmallestKeeper}<LEND>[statement 8; assign](){=}<LSEP>[](symbol){HighTrimPoint}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sortedDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){LargestKeeper}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){LowTrimPoint}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){writeLines}<LSEP>[argument 0; litteral](str){ERROR: The smallest FST in the...}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){HighTrimPoint}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){writeLines}<LSEP>[argument 0; litteral](str){ERROR: The largest FST in the ...}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LEND>[statement 11; assign](){=}<LSEP>[](symbol){putativeNeutralListTemp}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 12; assign](){=}<LSEP>[](symbol){oldOutlierFlag}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){FALSE}<LSEP>[](symbol){NLociTotal}<LEND>[statement 13; assign](){=}<LSEP>[](symbol){keepGoing}<LSEP>[litteral](logical){TRUE}<LEND>[statement 14; assign](){=}<LSEP>[](symbol){count}<LSEP>[litteral](real){0.000000}<LEND>[statement 15; control flow](){while}<LSEP>[](symbol){keepGoing}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){19.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){keepGoing}<LSEP>[litteral](logical){FALSE}<LEND>[statement 1; call](){}<LSEP>[](symbol){writeLines}<LSEP>[argument 0; litteral](str){Exceeded iteration maximum.}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){FstbarNoCorrTemp}<LEND>[call](){}<LSEP>[](symbol){fstBarCalculatorNoCorr}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){putativeNeutralListTemp}<LSEP>[](symbol){}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){dfInferredTemp}<LEND>[call](){}<LSEP>[](symbol){EffectiveNumberSamplesMLE}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){putativeNeutralListTemp}<LEND>[](symbol){FstbarNoCorrTemp}<LSEP>[](symbol){NumberOfSamples}<LSEP>[](symbol){LowTrimPoint}<LSEP>[](symbol){HighTrimPoint}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){workingDataFrame}<LEND>[call](){}<LSEP>[](symbol){pOutlierFinderChiSqNoCorr}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){FstbarNoCorrTemp}<LSEP>[](symbol){dfInferredTemp}<LSEP>[](symbol){qthreshold}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){OutlierFlag}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){LowTrimPoint}<LEND>[true branch; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){OutlierFlag}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[argument 1; litteral](real){0.000000}<LEND>[litteral](logical){TRUE}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){putativeNeutralListTemp}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){OutlierFlag}<LEND>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){putativeNeutralListTemp}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){writeLines}<LSEP>[argument 0; litteral](str){No loci in neutral list...}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](str){FAIL}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){oldOutlierFlag}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){OutlierFlag}<LEND>[true branch; assign](){=}<LSEP>[](symbol){keepGoing}<LSEP>[litteral](logical){FALSE}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){OutlierFlag}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){LowTrimPoint}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){writeLines}<LSEP>[argument 0; litteral](str){All loci with Fst below the lo...}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){OutlierFlag}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){HighTrimPoint}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){writeLines}<LSEP>[argument 0; litteral](str){All loci with Fst above the up...}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[statement 11; assign](){=}<LSEP>[](symbol){oldOutlierFlag}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){OutlierFlag}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){19.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){writeLines}<LSEP>[argument 0; litteral](str){Loop iteration limit exceeded.}<LEND>[statement 17; assign](){=}<LSEP>[](symbol){numberLowFstOutliers}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){OutlierFlag}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){LowTrimPoint}<LEND>[statement 18; assign](){=}<LSEP>[](symbol){numberHighFstOutliers}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){OutlierFlag}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){HighTrimPoint}<LEND>[statement 19; assign](){=}<LSEP>[](symbol){FSTbar}<LEND>[call](){}<LSEP>[](symbol){fstBarCalculator}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){putativeNeutralListTemp}<LSEP>[](symbol){}<LEND>[statement 20; assign](){=}<LSEP>[](symbol){resultsDataFrame}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){workingDataFrame}<LSEP>[](symbol){storedDataFrameNA}<LEND>[statement 21; assign](){=}<LSEP>[](symbol){resultsDataFrame}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){resultsDataFrame}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){resultsDataFrame}<LSEP>[](symbol){indexOrder}<LEND>[](symbol){}<LEND>[statement 22; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){FSTbar}<LSEP>[](symbol){FstbarNoCorrTemp}<LSEP>[](symbol){dfInferredTemp}<LSEP>[](symbol){numberLowFstOutliers}<LSEP>[](symbol){numberHighFstOutliers}<LSEP>[](symbol){resultsDataFrame}<LEND>[assign](){=}<LSEP>[](symbol){outputDFStarterNoCorr}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){FstDataFrame}<LSEP>[](symbol){Hmin}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){len}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){FstDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){indexOrder}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){len}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){GoodH}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){FstDataFrame}<LSEP>[](symbol){He}<LEND>[](symbol){Hmin}<LEND>[argument 1; litteral](str){lowH}<LSEP>[argument 2; litteral](str){goodH}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){OutlierFlag}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){FstDataFrame}<LSEP>[](symbol){FSTNoCorr}<LEND>[argument 1; litteral](logical){NA}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){qvalues}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){len}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){pvalues}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){len}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){pvaluesRightTail}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){len}<LEND>[statement 7; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){FstDataFrame}<LSEP>[](symbol){indexOrder}<LSEP>[](symbol){GoodH}<LSEP>[](symbol){qvalues}<LSEP>[](symbol){pvalues}<LSEP>[](symbol){pvaluesRightTail}<LSEP>[](symbol){OutlierFlag}<LEND>[assign](){=}<LSEP>[](symbol){pOutlierFinderChiSqNoCorr}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){DataList}<LSEP>[](symbol){Fstbar}<LSEP>[](symbol){dfInferred}<LSEP>[](symbol){qthreshold}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){DataListGood}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){DataList}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataList}<LSEP>[](symbol){FSTNoCorr}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](symbol){}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){DataListNonPosFst}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){DataList}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataList}<LSEP>[](symbol){FSTNoCorr}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](symbol){}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){DataListNA}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){DataList}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataList}<LSEP>[](symbol){FSTNoCorr}<LEND>[](symbol){}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){pList}<LEND>[call](){}<LSEP>[](symbol){pTwoSidedFromChiSq}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataListGood}<LSEP>[](symbol){FSTNoCorr}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){dfInferred}<LEND>[](symbol){Fstbar}<LEND>[](symbol){dfInferred}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){pListRightTail}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){pchisq}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataListGood}<LSEP>[](symbol){FSTNoCorr}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){dfInferred}<LEND>[](symbol){Fstbar}<LEND>[](symbol){dfInferred}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){qtemp}<LEND>[call](){}<LSEP>[](symbol){qvalue}<LSEP>[](symbol){pListRightTail}<LSEP>[](symbol){qthreshold}<LSEP>[argument 2; litteral](str){bootstrap}<LEND>[statement 6; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataListGood}<LSEP>[](symbol){pvalues}<LEND>[](symbol){pList}<LEND>[statement 7; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataListGood}<LSEP>[](symbol){pvaluesRightTail}<LEND>[](symbol){pListRightTail}<LEND>[statement 8; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataListGood}<LSEP>[](symbol){qvalues}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){qtemp}<LSEP>[](symbol){qvalues}<LEND>[statement 9; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){DataListGood}<LSEP>[](symbol){OutlierFlag}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){qtemp}<LSEP>[](symbol){significant}<LEND>[statement 10; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){DataListGood}<LSEP>[](symbol){DataListNonPosFst}<LSEP>[](symbol){DataListNA}<LEND>[assign](){=}<LSEP>[](symbol){pTwoSidedFromChiSq}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){df}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){pOneSided}<LEND>[call](){}<LSEP>[](symbol){pchisq}<LSEP>[](symbol){x}<LSEP>[](symbol){df}<LEND>[statement 1; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){pOneSided}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){pOneSided}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){pOneSided}<LSEP>[argument 1; litteral](real){2.000000}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){is.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){folder}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}