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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.report.rdepth}<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){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){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){!}<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){loc.metrics}<LEND>[](symbol){AvgReadDepth}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rdepth}<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){AvgReadDepth}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Read depth not in...}<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){!}<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){loc.metrics}<LEND>[](symbol){rdepth}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rdepth}<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){rdepth}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Read depth not in...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){lower}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){rdepth}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){upper}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){rdepth}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<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 read depth: }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){rdepth}<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 read depth: }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){rdepth}<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 read depth: }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){rdepth}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; litteral](str){\n\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){upper}<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){rdepth}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){rdepth}<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; 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; litteral](str){m}<LEND>[statement 27; 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)\nRead Depth...}<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 28; 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 29; 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 30; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){boxplot}<LSEP>[argument 1; litteral](str){standard}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whisker}<LEND>[call](){}<LSEP>[](symbol){boxplot}<LSEP>[](symbol){rdepth}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){red}<LSEP>[](symbol){range}<LSEP>[](symbol){title}<LEND>[statement 1; 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; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Standard boxplot, no adjustm...}<LEND>[statement 1; 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}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){loc.names}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){rdepth}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Standard boxplot, no adjustm...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whisker}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){robustbase}<LSEP>[](symbol){adjbox}<LEND>[](symbol){rdepth}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){red}<LSEP>[](symbol){range}<LSEP>[](symbol){title}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Boxplot adjusted to account ...}<LEND>[statement 1; 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}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){loc.names}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){rdepth}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Boxplot adjusted to account ...}<LEND>[statement 31; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[argument 1; litteral](real){0.500000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[statement 32; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){rdepth}<LSEP>[argument 1; litteral](str){red}<LSEP>[argument 2; litteral](real){100.000000}<LSEP>[argument 3; litteral](NULL){NULL}<LEND>[statement 33; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No outliers detected\n}<LEND>[false 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){ Outliers detected -- returne...}<LEND>[statement 34; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){op}<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}<LSEP>[](symbol){outliers}

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call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Standard boxplot, no adjus...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whisker}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){robustbase}<LSEP>[](symbol){adjbox}<LEND>[](symbol){nchar.tags}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){red}<LSEP>[](symbol){range}<LSEP>[argument 4; litteral](str){Tag Length}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Boxplot adjusted to accoun...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outliers}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){loc.names}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){nchar.tags}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Boxplot adjusted to accoun...}<LEND>[statement 31; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[argument 1; litteral](real){0.500000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[statement 32; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){nchar.tags}<LSEP>[argument 1; litteral](str){red}<LSEP>[argument 2; litteral](real){100.000000}<LSEP>[argument 3; litteral](NULL){NULL}<LEND>[statement 33; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No outliers detected\n}<LEND>[false 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){ Outliers detected -- \n}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){outliers}<LEND>[statement 34; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){op}<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; 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; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](NULL){NULL}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){outliers}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){print.discdd.misclass}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){dist.print}<LSEP>[](symbol){prox.print}<LSEP>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){alloc}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){confusion.mat}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rsums}<LEND>[call](){}<LSEP>[](symbol){rowSums}<LSEP>[](symbol){alloc}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){csums}<LEND>[call](){}<LSEP>[](symbol){colSums}<LSEP>[](symbol){alloc}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){wellclass}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){alloc}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){namesalloc}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){alloc}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){alloc}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){alloc}<LSEP>[](symbol){rsums}<LEND>[argument 2; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){wellclass}<LSEP>[](symbol){rsums}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){alloc}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){alloc}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){csums}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){csums}<LEND>[argument 2; litteral](logical){NA}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){alloc}<LEND>[](symbol){namesalloc}<LEND>[statement 8; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\nmisallocation ratio: }<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){misclassed}<LEND>[argument 2; litteral](str){\n\n}<LEND>[statement 9; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){alloc}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){...}<LEND>[statement 10; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 11; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){classification}<LEND>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){...}<LEND>[statement 12; control flow](){if}<LSEP>[](symbol){dist.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){distances between groups and c...}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){distances}<LEND>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 13; control flow](){if}<LSEP>[](symbol){prox.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){groups-classes proximity index\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){proximities}<LEND>[](symbol){...}<LEND>[statement 14; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){ddjensenpar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){p1}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){p2}<LEND>[](symbol){k}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p1 and p2 must have the same n...}<LEND>[statement 2; 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){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){p2}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p1 and p2 must be vectors with...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dinv}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dd1}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p1}<LSEP>[](symbol){dinv}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dd2}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p2}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){p2}<LSEP>[](symbol){dinv}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){dd1}<LSEP>[](symbol){dd2}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dd1}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){p1}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dd2}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){p2}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){p2}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){dd1}<LSEP>[](symbol){dd2}<LEND>[argument 1; litteral](logical){TRUE}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){utils.recalc.maf}<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; assign](){<-}<LSEP>[](symbol){hold}<LSEP>[](symbol){x}<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; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){ddchisqsympar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){p1}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){p2}<LEND>[](symbol){k}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p1 and p2 must have the same n...}<LEND>[statement 2; 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){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){p2}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p1 and p2 must be vectors with...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dd}<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){p1}<LSEP>[](symbol){p2}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){dd}<LEND>[litteral](logical){NA}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){dd}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dd}<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){as.numeric}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){p2}<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){as.numeric}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){p2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){dd}<LEND>[litteral](logical){NA}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){dd}<LSEP>[argument 1; litteral](logical){TRUE}

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litteral](str){l}<LEND>[statement 8; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d.l}<LSEP>[](symbol){cellmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d.l}<LSEP>[](symbol){upr}<LEND>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){1.000000}<LSEP>[argument 4; litteral](str){black}<LSEP>[argument 5; litteral](str){l}<LEND>[statement 9; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d.r}<LSEP>[](symbol){cellmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d.r}<LSEP>[](symbol){est}<LEND>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](str){black}<LSEP>[argument 5; litteral](str){l}<LEND>[statement 10; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d.r}<LSEP>[](symbol){cellmp}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d.r}<LSEP>[](symbol){lwr}<LEND>[argument 2; 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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 17; 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 18; 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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>[litteral](str){NJM_WC}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plotRadar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){layer}<LSEP>[](symbol){main}<LSEP>[](symbol){land}<LSEP>[](symbol){sea}<LSEP>[](symbol){de}<LSEP>[](symbol){eu}<LSEP>[](symbol){col}<LSEP>[](symbol){xlim}<LSEP>[](symbol){ylim}<LSEP>[](symbol){zlim}<LSEP>[](symbol){axes}<LSEP>[](symbol){las}<LSEP>[](symbol){mar}<LSEP>[](symbol){keeppar}<LSEP>[](symbol){project}<LSEP>[](symbol){proj}<LSEP>[](symbol){extent}<LSEP>[](symbol){adjust05}<LSEP>[](symbol){targetproj}<LSEP>[](symbol){quiet}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){checkSuggestedPackage}<LSEP>[argument 0; litteral](str){raster}<LSEP>[argument 1; litteral](str){plotRadar}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){dat}<LSEP>[argument 1; litteral](str){meta}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){plotRadar needs the 'dat' elem...}<LEND>[statement 2; call](){}<LSEP>[](symbol){force}<LSEP>[](symbol){main}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){layer}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){layer}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){title}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){main}<LEND>[statement 5; control flow](){if}<LSEP>[](symbol){project}<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){- projecting:}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){projectRasterDWD}<LSEP>[](symbol){x}<LSEP>[](symbol){proj}<LSEP>[](symbol){extent}<LSEP>[](symbol){adjust05}<LSEP>[](symbol){targetproj}<LSEP>[](symbol){quiet}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){- preparing plots...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){ext}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){extent}<LEND>[](symbol){x}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){xlim}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){xlim}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){ext}<LSEP>[](symbol){xmin}<LEND>[argument 1; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){ext}<LSEP>[](symbol){xmax}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ylim}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){ylim}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){ext}<LSEP>[](symbol){ymin}<LEND>[argument 1; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){ext}<LSEP>[](symbol){ymax}<LEND>[statement 10; call](){}<LSEP>[](symbol){load}<LEND>[argument 0; call](){}<LSEP>[](symbol){system.file}<LSEP>[argument 0; litteral](str){extdata/DEU.rda}<LSEP>[argument 1; litteral](str){rdwd}<LEND>[argument 1; call](){}<LSEP>[](symbol){environment}<LEND>[statement 11; call](){}<LSEP>[](symbol){load}<LEND>[argument 0; call](){}<LSEP>[](symbol){system.file}<LSEP>[argument 0; litteral](str){extdata/EUR.rda}<LSEP>[argument 1; litteral](str){rdwd}<LEND>[argument 1; call](){}<LSEP>[](symbol){environment}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){singlemap}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x_i}<LSEP>[](symbol){main_i}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){plot}<LEND>[](symbol){DEU}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[](symbol){xlim}<LSEP>[](symbol){ylim}<LSEP>[](symbol){axes}<LSEP>[](symbol){las}<LEND>[statement 1; call](){}<LSEP>[](symbol){rect}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){usr}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){usr}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){usr}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){usr}<LEND>[argument 1; litteral](real){4.000000}<LEND>[](symbol){sea}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){plot}<LEND>[](symbol){EUR}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){land}<LEND>[statement 3; call](){}<LSEP>[](symbol){box}<LEND>[statement 4; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){plot}<LEND>[](symbol){x_i}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){zlim}<LSEP>[](symbol){col}<LSEP>[](symbol){...}<LEND>[statement 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){plot}<LEND>[](symbol){DEU}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){de}<LEND>[statement 6; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){plot}<LEND>[](symbol){EUR}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){eu}<LEND>[statement 7; call](){}<LSEP>[](symbol){title}<LSEP>[](symbol){main_i}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){lay}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){nlayers}<LEND>[](symbol){x}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){lay2}<LSEP>[](symbol){lay}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){main}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){main}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lay}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){layer}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){lay}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lay}<LSEP>[](symbol){layer}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){nn}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){lay}<LSEP>[](symbol){lay2}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nn}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[](symbol){nn}<LSEP>[argument 1; litteral](str){ layer}<LEND>[argument 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nn}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; litteral](str){s}<LEND>[argument 3; litteral](str){ selected that do}<LEND>[argument 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){nn}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; litteral](str){es}<LEND>[argument 5; litteral](str){ not exist.}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){zlim}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){zlim}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){cellStats}<LEND>[](symbol){x}<LSEP>[](symbol){range}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){zlim}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){zlim}<LEND>[call](){}<LSEP>[](symbol){range}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){zlim}<LSEP>[](symbol){}<LSEP>[](symbol){lay}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){zlim}<LSEP>[argument 1; litteral](str){ind}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){zlim}<LSEP>[litteral](NULL){NULL}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){op}<LEND>[call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){mar}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){keeppar}<LEND>[true branch; call](){}<LSEP>[](symbol){on.exit}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){op}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){lapply}<LEND>[call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){pbapply}<LSEP>[](symbol){pblapply}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){- plotting }<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lay}<LEND>[argument 2; litteral](str){ layer}<LEND>[argument 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lay}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; litteral](str){s}<LEND>[argument 4; litteral](str){:}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){dummy}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){lay}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; call](){}<LSEP>[](symbol){singlemap}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){main}<LSEP>[](symbol){i}<LEND>[statement 27; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl2sa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){verbose}<LSEP>[](symbol){installed}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sa}<LSEP>[litteral](NULL){NULL}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){installed}<LEND>[true branch; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){This function requires the pac...}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){target_diagram}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){data}<LSEP>[](symbol){xlab}<LSEP>[](symbol){ylab}<LSEP>[](symbol){type}<LSEP>[](symbol){cuts}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){prepareData}<LSEP>[](symbol){data}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){circle}<LEND>[call](){}<LSEP>[](symbol){makeCircles}<LSEP>[](symbol){data}<LSEP>[](symbol){type}<LSEP>[](symbol){cuts}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){radius}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){circle}<LSEP>[](symbol){r}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){labels}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){radius}<LEND>[argument 2; call](){}<LSEP>[](symbol){signif}<LSEP>[](symbol){radius}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 4; 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){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ggplot}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_point}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes_string}<LSEP>[argument 0; litteral](str){nrmsec*sign(difSD)}<LSEP>[argument 1; litteral](str){nmbe}<LSEP>[](symbol){...}<LEND>[argument 2; litteral](str){black}<LSEP>[argument 3; litteral](real){21.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_path}<LEND>[argument 0; call](){}<LSEP>[](symbol){aes_string}<LSEP>[argument 0; litteral](str){x}<LSEP>[argument 1; litteral](str){y}<LEND>[](symbol){circle}<LSEP>[argument 2; litteral](str){gray}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_vline}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](str){gray}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_hline}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](str){gray}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_text}<LEND>[argument 0; call](){}<LSEP>[](symbol){aes_string}<LSEP>[argument 0; litteral](str){x}<LSEP>[argument 1; litteral](str){y}<LSEP>[argument 2; litteral](str){lbs}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[argument 1; litteral](real){3.000000}<LSEP>[](symbol){labels}<LEND>[argument 1; call](){}<LSEP>[](symbol){xlab}<LSEP>[](symbol){xlab}<LEND>[argument 1; call](){}<LSEP>[](symbol){ylab}<LSEP>[](symbol){ylab}<LEND>[argument 1; call](){}<LSEP>[](symbol){coord_fixed}<LEND>[argument 1; call](){}<LSEP>[](symbol){theme_bw}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matddjeffreys}<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){ddjeffreys}<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){mrdwt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){L}<LEND>[body; block](){}<LSEP>[statement 0; call](){.Call}<LSEP>[call name; litteral](str){do_mrdwt}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.vector}<LSEP>[](symbol){h}<LEND>[argument 2; call](){}<LSEP>[](symbol){as.integer}<LSEP>[](symbol){L}<LEND>[argument 3; litteral](str){rwt}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.pkgenv}<LEND>[call](){}<LSEP>[](symbol){new.env}<LEND>[argument 0; call](){}<LSEP>[](symbol){emptyenv}<LEND>[assign](){<-}<LSEP>[](symbol){.defaultFile}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){getRversion}<LEND>[argument 1; litteral](str){4.0.0}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tddir}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tools}<LSEP>[](symbol){R_user_dir}<LEND>[argument 0; litteral](str){td}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){dir.exists}<LSEP>[](symbol){tddir}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fname}<LEND>[call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){tddir}<LSEP>[argument 1; litteral](str){api.dcf}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){file.exists}<LSEP>[](symbol){fname}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){fname}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](str){}<LEND>[assign](){<-}<LSEP>[](symbol){.getKeyIntoPkgEnv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){silent}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){.pkgenv}<LSEP>[argument 1; litteral](str){api}<LEND>[litteral](str){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){fname}<LEND>[call](){}<LSEP>[](symbol){.defaultFile}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){fname}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){read.dcf}<LSEP>[](symbol){fname}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[argument 0; litteral](str){key}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){res}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){.pkgenv}<LSEP>[argument 1; litteral](str){api}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){res}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](str){key}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){silent}<LEND>[true branch; call](){}<LSEP>[](symbol){packageStartupMessage}<LSEP>[argument 0; litteral](str){Setting API key from config file.}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){silent}<LEND>[true branch; call](){}<LSEP>[](symbol){packageStartupMessage}<LSEP>[argument 0; litteral](str){API key file found but no api ...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; assign](){<-}<LSEP>[](symbol){ev}<LEND>[call](){}<LSEP>[](symbol){Sys.getenv}<LSEP>[argument 0; litteral](str){TWELVEDATA_API_KEY}<LEND>[argument 1; litteral](str){}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){.pkgenv}<LSEP>[argument 1; litteral](str){api}<LEND>[](symbol){ev}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){silent}<LEND>[true branch; call](){}<LSEP>[](symbol){packageStartupMessage}<LSEP>[argument 0; litteral](str){Setting API key from environme...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){silent}<LEND>[true branch; call](){}<LSEP>[](symbol){packageStartupMessage}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){No config file or environment ...}<LSEP>[argument 1; litteral](str){found: API access unlikely.}<LEND>[assign](){<-}<LSEP>[](symbol){.onLoad}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){libname}<LSEP>[](symbol){pkgname}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){.getKeyIntoPkgEnv}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[assign](){<-}<LSEP>[](symbol){.onAttach}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){libname}<LSEP>[](symbol){pkgname}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){packageStartupMessage}<LSEP>[argument 0; litteral](str){Attaching td version }<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){utils}<LSEP>[](symbol){packageVersion}<LEND>[argument 0; litteral](str){td}<LEND>[argument 2; litteral](str){. }<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 1; call](){}<LSEP>[](symbol){.getKeyIntoPkgEnv}<LSEP>[argument 0; litteral](logical){FALSE}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){nearbyStations}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){lat}<LSEP>[](symbol){lon}<LSEP>[](symbol){radius}<LSEP>[](symbol){res}<LSEP>[](symbol){var}<LSEP>[](symbol){per}<LSEP>[](symbol){mindate}<LSEP>[](symbol){hasfileonly}<LSEP>[](symbol){statname}<LSEP>[](symbol){quiet}<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){lat}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){lat mus be a single value, not }<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lat}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lon}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){lon mus be a single value, not }<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lon}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){lon}<LSEP>[](symbol){lat}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){lon>lat, but lon should be sma...}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){mindate}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){mindate mus be a single value,...}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){mindate}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){radius}<LSEP>[argument 1; litteral](real){1000.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){radius is supposed to be given...}<LSEP>[argument 1; litteral](str){Your value seems irreasonably ...}<LSEP>[](symbol){radius}<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){Selecting stations...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){m}<LSEP>[](symbol){metaIndex}<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){hasfileonly}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){hasfile}<LEND>[](symbol){}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){res}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){res}<LEND>[](symbol){res}<LEND>[](symbol){}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){var}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){var}<LEND>[](symbol){var}<LEND>[](symbol){}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){per}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){per}<LEND>[](symbol){per}<LEND>[](symbol){}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){mindate}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){bis_datum}<LEND>[](symbol){mindate}<LEND>[](symbol){}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){m}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){geoBreite}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){lat}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){geoLaenge}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){lon}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){Stationsname}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){statname}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){res}<LEND>[argument 1; litteral](real){1.000000}<LEND>[litteral](str){z}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){m}<LEND>[argument 1; litteral](real){1.000000}<LEND>[litteral](str){Target}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){dist}<LEND>[call](){}<LSEP>[](symbol){lldist}<LSEP>[argument 0; litteral](str){geoBreite}<LSEP>[argument 1; litteral](str){geoLaenge}<LSEP>[](symbol){m}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){dist}<LEND>[](symbol){radius}<LEND>[](symbol){}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){sortDF}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](str){dist}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){m}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No data was found for this que...}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.report.overshoot}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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; 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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 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){method}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SNP}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){method}<LSEP>[litteral](str){Euclidean}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; 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litteral](str){euclidean}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stats}<LSEP>[](symbol){dist}<LEND>[](symbol){x}<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 Euclidean Distan...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){locus.count}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ape}<LSEP>[](symbol){dist.gene}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){pairwise}<LSEP>[argument 2; 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assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){dd}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){ord}<LEND>[call](){}<LSEP>[](symbol){rank}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){dd}<LEND>[](symbol){ord}<LSEP>[](symbol){ord}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){mat}<LEND>[statement 16; 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){method}<LSEP>[argument 1; litteral](str){simple}<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){ Calculating the Simple Match...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){jaccard}<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){ Calculating the Jaccard Index\n}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){dice}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matddlp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){p}<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){ddlp}<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>[](symbol){p}<LEND>[statement 4; call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){distances}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.report.RepAvg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){boxplot}<LSEP>[](symbol){range}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: This function will be...}<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){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; 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litteral](str){ Fatal Error: genlight object...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence ...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Terminating Execution!}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){hold}<LSEP>[](symbol){x}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){repeatability}<LEND>[call](){}<LSEP>[](symbol){$}<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 10; assign](){<-}<LSEP>[](symbol){xlimit}<LEND>[call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){repeatability}<LEND>[statement 11; 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 12; 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 13; 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 14; 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 15; 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 16; assign](){<-}<LSEP>[](symbol){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){pc.retained}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){21.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){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){pc.filtered}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){21.000000}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){percentile}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](real){21.000000}<LEND>[statement 21; 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; 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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 22; 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 23; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){df}<LEND>[statement 24; 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 25; 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 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){df}<LEND>[litteral](NULL){NULL}<LEND>[statement 27; 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 28; 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[](){expression}<LSEP>[litteral](str){Hurricane}

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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rt_ticket_merge}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){origin}<LSEP>[](symbol){into}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){url}<LEND>[call](){}<LSEP>[](symbol){rt_url}<LSEP>[argument 0; litteral](str){ticket}<LSEP>[](symbol){origin}<LSEP>[argument 2; litteral](str){merge}<LSEP>[](symbol){into}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){response}<LEND>[call](){}<LSEP>[](symbol){rt_POST}<LSEP>[](symbol){url}<LEND>[statement 2; call](){}<LSEP>[](symbol){stopforstatus}<LSEP>[](symbol){response}<LEND>[statement 3; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[statement 4; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){into}