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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){summary.foldermtg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i.vertices}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; 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){object}<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 1; assign](){<-}<LSEP>[](symbol){value}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){object}<LSEP>[](symbol){i.vertices}<LEND>[](symbol){summary}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){value}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){verboseApply}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LSEP>[](symbol){.mc}<LSEP>[](symbol){.mapper}<LSEP>[](symbol){.bar}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stopifnot}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.element}<LSEP>[](symbol){.bar}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){none}<LSEP>[argument 1; litteral](str){.}<LSEP>[argument 2; litteral](str){bar}<LEND>[statement 1; call](){}<LSEP>[](symbol){stopifnot}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){.mc}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){.mc}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){initStatusBar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){n}<LSEP>[](symbol){step}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pb}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){progress}<LSEP>[](symbol){progress_bar}<LEND>[](symbol){new}<LEND>[](symbol){n}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pb}<LSEP>[](symbol){tick}<LEND>[](symbol){step}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){bar}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){.bar}<LSEP>[argument 1; litteral](str){none}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LSEP>[body; litteral](NULL){NULL}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){.bar}<LSEP>[argument 1; litteral](str){.}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){.}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){.bar}<LSEP>[argument 1; litteral](str){bar}<LEND>[true branch; call](){}<LSEP>[](symbol){initStatusBar}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[](symbol){.mc}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){fun}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){f}<LSEP>[](symbol){...}<LEND>[statement 1; call](){}<LSEP>[](symbol){bar}<LEND>[](symbol){res}<LEND>[statement 5; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){as.function}<LSEP>[](symbol){.mapper}<LEND>[](symbol){x}<LSEP>[](symbol){fun}<LSEP>[](symbol){...}<LSEP>[](symbol){.mc}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.dist.pop}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){method}<LSEP>[](symbol){plot}<LSEP>[](symbol){boxplot}<LSEP>[](symbol){range}<LSEP>[](symbol){binary}<LSEP>[](symbol){p}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pkg}<LSEP>[litteral](str){reshape2}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){requireNamespace}<LSEP>[](symbol){pkg}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Package}<LSEP>[](symbol){pkg}<LSEP>[argument 2; litteral](str){ needed for this function to w...}<LEND>[false branch; 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; assign](){<-}<LSEP>[](symbol){veganmethod}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){bray}<LSEP>[argument 1; litteral](str){kulczynski}<LSEP>[argument 2; litteral](str){jaccard}<LSEP>[argument 3; litteral](str){gower}<LSEP>[argument 4; litteral](str){morisita}<LSEP>[argument 5; litteral](str){horn}<LSEP>[argument 6; litteral](str){mountford}<LSEP>[argument 7; litteral](str){raup}<LSEP>[argument 8; litteral](str){binomial}<LSEP>[argument 9; litteral](str){chao}<LSEP>[argument 10; litteral](str){cao}<LSEP>[argument 11; litteral](str){mahalanobis}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){distmethod}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){euclidean}<LSEP>[argument 1; litteral](str){maximum}<LSEP>[argument 2; litteral](str){manhattan}<LSEP>[argument 3; litteral](str){canberra}<LSEP>[argument 4; litteral](str){binary}<LSEP>[argument 5; litteral](str){minkowski}<LSEP>[argument 6; litteral](str){Chebyshev}<LEND>[statement 9; 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){%in%}<LSEP>[](symbol){method}<LSEP>[](symbol){veganmethod}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){method}<LSEP>[](symbol){distmethod}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){pcfixed}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Specified distanc...}<LSEP>[](symbol){veganmethod}<LSEP>[](symbol){distmethod}<LSEP>[argument 3; litteral](str){or 'pcfixed'\n}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){hard.min.p}<LSEP>[litteral](real){0.250000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){m}<LSEP>[](symbol){method}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){b}<LSEP>[](symbol){binary}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){pr}<LSEP>[](symbol){p}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){u}<LSEP>[litteral](logical){TRUE}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){d}<LSEP>[litteral](logical){TRUE}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){gl.percent.freq}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){f}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){6.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){reshape2}<LSEP>[](symbol){dcast}<LEND>[](symbol){f}<LEND>[argument 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){popn}<LSEP>[](symbol){locus}<LEND>[argument 2; litteral](str){frequency}<LEND>[statement 19; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){f}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){f}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){m}<LSEP>[](symbol){distmethod}<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}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Calculating distances: }<LSEP>[](symbol){m}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Refer to dist {stats} docume...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){minkowski}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){pr}<LSEP>[argument 1; litteral](real){0.250000}<LEND>[true branch; block](){}<LSEP>[statement 0; 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){ Warning:}<LSEP>[](symbol){hard.min.p}<LSEP>[argument 2; litteral](str){is the practical minimum for M...}<LSEP>[](symbol){hard.min.p}<LSEP>[argument 4; litteral](str){\n\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pr}<LSEP>[](symbol){hard.min.p}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){pr}<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){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Note: for p = 1, Minkowski d...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){pr}<LSEP>[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){ Note: for p = 2, Minkowski d...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){pr}<LSEP>[argument 1; litteral](real){30.000000}<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){ Note: for large p, Minkowski...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){pr}<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){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Note: for p < 1, Minkowski d...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stats}<LSEP>[](symbol){dist}<LEND>[](symbol){f}<LSEP>[](symbol){m}<LSEP>[](symbol){d}<LSEP>[](symbol){u}<LSEP>[](symbol){pr}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){m}<LSEP>[](symbol){veganmethod}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){vegan}<LSEP>[](symbol){vegdist}<LEND>[](symbol){f}<LSEP>[](symbol){m}<LSEP>[](symbol){b}<LSEP>[](symbol){d}<LSEP>[](symbol){u}<LSEP>[argument 5; litteral](logical){TRUE}<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}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Calculating distances: }<LSEP>[](symbol){m}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Refer to vegdist {vegan} d...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){bray}<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){ Note: the Bray-Curtis distan...}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](str){pcfixed}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){gl.fixed.diff}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[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 percent fixed di...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Note: this distance may be non...}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){dd}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){ord}<LEND>[call](){}<LSEP>[](symbol){rank}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[statement 27; 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 28; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){mat}<LEND>[statement 29; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; 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 1; 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 2; 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)\nPopulation }<LSEP>[](symbol){method}<LSEP>[argument 2; litteral](str){ Distances}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){title}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Tag P/A data (SilicoDArT)\nPop...}<LSEP>[](symbol){method}<LSEP>[argument 2; litteral](str){ Distances}<LEND>[statement 3; 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){dd}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){red}<LSEP>[](symbol){range}<LSEP>[](symbol){title}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Standard boxplot, no adjustm...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){robustbase}<LSEP>[](symbol){adjbox}<LEND>[](symbol){dd}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){red}<LSEP>[](symbol){range}<LSEP>[](symbol){title}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Boxplot adjusted to account ...}<LEND>[statement 4; 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 5; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){dd}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){blue}<LSEP>[argument 4; litteral](str){red}<LEND>[argument 5; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){dd}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){dd}<LEND>[argument 6; litteral](real){100.000000}<LEND>[statement 30; 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 Reporting inter-population...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Distance measure:}<LSEP>[](symbol){method}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 2; 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}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Average no. of individuals...}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 4; 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 5; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Miniumum Distance: }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){dd}<LEND>[argument 1; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){store_key}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){apikey}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){R.version.string}<LSEP>[argument 1; litteral](str){4.0.0}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){This function relies on R vers...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; 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 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){dir.exists}<LSEP>[](symbol){tddir}<LEND>[true branch; call](){}<LSEP>[](symbol){dir.create}<LSEP>[](symbol){tddir}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){fname}<LEND>[call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){tddir}<LSEP>[argument 1; litteral](str){api2.dcf}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){file.exists}<LSEP>[](symbol){fname}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Existing file found, so overwr...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){con}<LEND>[call](){}<LSEP>[](symbol){file}<LSEP>[](symbol){fname}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){key:}<LSEP>[](symbol){apikey}<LSEP>[](symbol){con}<LEND>[statement 7; call](){}<LSEP>[](symbol){close}<LSEP>[](symbol){con}<LEND>[statement 8; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[assign](){<-}<LSEP>[](symbol){.get_apikey}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){apikey}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){.pkgenv}<LSEP>[argument 1; litteral](str){api}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){apikey}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No query without key.}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[](symbol){apikey}

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

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){wassersteinpar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){mean1}<LSEP>[](symbol){var1}<LSEP>[](symbol){mean2}<LSEP>[](symbol){var2}<LSEP>[](symbol){check}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){mean1}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mean1}<LSEP>[](symbol){mean2}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vars}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){var1}<LSEP>[](symbol){var2}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){check}<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){abs}<LSEP>[](symbol){var1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){var2}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){At least one variance is zero}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){sqrt}<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){d}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){var1}<LEND>[](symbol){var2}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){var1}<LSEP>[](symbol){var2}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){check}<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){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LSEP>[](symbol){var1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LSEP>[](symbol){var2}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){One of the sample variances is...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sqrtvar2}<LEND>[call](){}<LSEP>[](symbol){sqrtmatrix}<LSEP>[](symbol){var2}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){sqrtvars}<LEND>[call](){}<LSEP>[](symbol){sqrtmatrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%*%}<LSEP>[](symbol){sqrtvar2}<LSEP>[](symbol){var1}<LEND>[](symbol){sqrtvar2}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tracevar}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){vars}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){sqrtvars}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){d}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){tracevar}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.recode.ind}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){ind.recode}<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; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){addtest}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){test.x}<LSEP>[](symbol){test.y}<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){x}<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; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){test.y}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){This funciton needs a tesing r...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){test.x}<LEND>[true branch; block](){}<LSEP>[statement 0; 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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 (DArTSeq)\nCall Rate ...}<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 (SilicoDArT)...}<LEND>[statement 2; 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){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ggplot}<LEND>[argument 0; call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){ind.call.rate}<LEND>[argument 1; 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call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Miniumum Call Rate: }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){ind.call.rate}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Maximum Call Rate: }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){ind.call.rate}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 10; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Average Call Rate: }<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){ind.call.rate}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 11; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.report.hwe}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){subset}<LSEP>[](symbol){plot}<LSEP>[](symbol){method}<LSEP>[](symbol){alpha}<LSEP>[](symbol){bonf}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pkg}<LSEP>[litteral](str){HardyWeinberg}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){requireNamespace}<LSEP>[](symbol){pkg}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Package}<LSEP>[](symbol){pkg}<LSEP>[argument 2; litteral](str){ needed for this function to w...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; 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litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){a}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){Hom_1}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){Het}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){a}<LSEP>[](symbol){Hom_2}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){AA}<LSEP>[argument 1; litteral](str){AB}<LSEP>[argument 2; litteral](str){BB}<LEND>[statement 9; control flow](){if}<LSEP>[](symbol){bonf}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){c.alpha}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){alpha}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xlabel}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Population: }<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){c.alpha}<LSEP>[](symbol){alpha}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xlabel}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Population: }<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){Fisher}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){HardyWeinberg}<LSEP>[](symbol){HWTernaryPlot}<LEND>[](symbol){mat}<LSEP>[argument 1; litteral](real){100.000000}<LSEP>[argument 2; litteral](real){7.000000}<LSEP>[argument 3; litteral](real){1.250000}<LSEP>[](symbol){c.alpha}<LSEP>[argument 5; litteral](logical){TRUE}<LSEP>[argument 6; litteral](logical){TRUE}<LSEP>[](symbol){xlabel}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){HardyWeinberg}<LSEP>[](symbol){HWTernaryPlot}<LEND>[](symbol){mat}<LSEP>[argument 1; litteral](real){100.000000}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){1.250000}<LSEP>[](symbol){c.alpha}<LSEP>[argument 5; litteral](logical){TRUE}<LSEP>[argument 6; litteral](logical){TRUE}<LSEP>[](symbol){xlabel}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){rprob}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){Prob}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){result}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){rprob}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){rprob}<LSEP>[](symbol){alpha}<LEND>[](symbol){}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){result}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){Locus}<LEND>[](symbol){}<LEND>[statement 16; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Reporting significant depa...}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){result}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No significant departures\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ NB: Departures significant...}<LSEP>[](symbol){alpha}<LSEP>[argument 2; litteral](str){are listed\n}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){alpha}<LSEP>[argument 1; litteral](real){0.050000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ ns --}<LSEP>[](symbol){alpha}<LSEP>[argument 2; litteral](str){< p < 0.05; * -- 0.05 < p < 0....}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ ns -- p > 0.05; * -- 0.0...}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Critical values for signif...}<LEND>[statement 3; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){result}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 18; 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 19; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){result}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){ddlppar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LSEP>[](symbol){p}<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){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LEND>[](symbol){p}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){dd}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<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>[](symbol){p}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){dd}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){is.discdd.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){discdd.predict}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){RRR_sim}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){N}<LSEP>[](symbol){P}<LSEP>[](symbol){Q}<LSEP>[](symbol){R}<LSEP>[](symbol){r}<LSEP>[](symbol){mu}<LSEP>[](symbol){A}<LSEP>[](symbol){B}<LSEP>[](symbol){D}<LSEP>[](symbol){varcov}<LSEP>[](symbol){innov}<LSEP>[](symbol){mean_x}<LSEP>[](symbol){mean_z}<LSEP>[](symbol){x}<LSEP>[](symbol){z}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){P}<LEND>[argument 1; call](){}<LSEP>[](symbol){NROW}<LSEP>[](symbol){A}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){P is not the same with the row...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){Q}<LEND>[argument 1; call](){}<LSEP>[](symbol){NROW}<LSEP>[](symbol){B}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Q is not the same with the row...}<LEND>[statement 2; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){CasColNames}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){df}<LSEP>[](symbol){restore}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){NewColnames}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){GroupCode}<LSEP>[argument 1; litteral](str){Company}<LSEP>[argument 2; litteral](str){AccidentYear}<LSEP>[argument 3; litteral](str){DevelopmentYear}<LSEP>[argument 4; litteral](str){Lag}<LSEP>[argument 5; litteral](str){CumulativeIncurred}<LSEP>[argument 6; litteral](str){CumulativePaid}<LSEP>[argument 7; litteral](str){IBNR}<LSEP>[argument 8; litteral](str){DirectEP}<LSEP>[argument 9; litteral](str){CededEP}<LSEP>[argument 10; litteral](str){NetEP}<LSEP>[argument 11; litteral](str){Single}<LSEP>[argument 12; litteral](str){Reserve1997}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){OldColnames}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){GRCODE}<LSEP>[argument 1; litteral](str){GRNAME}<LSEP>[argument 2; litteral](str){AccidentYear}<LSEP>[argument 3; litteral](str){DevelopmentYear}<LSEP>[argument 4; litteral](str){DevelopmentLag}<LSEP>[argument 5; litteral](str){IncurLoss_D}<LSEP>[argument 6; litteral](str){CumPaidLoss_D}<LSEP>[argument 7; litteral](str){BulkLoss_D}<LSEP>[argument 8; litteral](str){EarnedPremDIR_D}<LSEP>[argument 9; litteral](str){EarnedPremCeded_D}<LSEP>[argument 10; litteral](str){EarnedPremNet_D}<LSEP>[argument 11; litteral](str){Single}<LSEP>[argument 12; litteral](str){PostedReserve97_D}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){restore}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){df}<LEND>[](symbol){OldColnames}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){df}<LEND>[](symbol){NewColnames}<LEND>[](symbol){df}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl2svdquartets}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){outfile}<LSEP>[](symbol){outpath}<LSEP>[](symbol){method}<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){outfile}<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; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.sim.ind}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){gl}<LSEP>[](symbol){n}<LSEP>[](symbol){popname}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){gl}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){alf}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LSEP>[](symbol){p}<LSEP>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){alfinds}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){alf}<LSEP>[](symbol){n}<LEND>[](symbol){n}<LSEP>[](symbol){T}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){simind}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){alfinds}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; 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){1.000000}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){glsim}<LEND>[call](){}<LSEP>[](symbol){new}<LSEP>[argument 0; litteral](str){genlight}<LSEP>[](symbol){simind}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[argument 4; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){gl}<LEND>[argument 5; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){loc.all}<LEND>[argument 6; call](){}<LSEP>[](symbol){position}<LSEP>[](symbol){gl}<LEND>[argument 7; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){popname}<LSEP>[](symbol){n}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){glsim}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){appendtofolderh}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fh}<LSEP>[](symbol){df}<LSEP>[](symbol){key}<LSEP>[](symbol){after}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){name.fh}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){fh}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){name.df}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){df}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folderh}<LSEP>[](symbol){fh}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fh must be an object of class ...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){key}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){df}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){There is no }<LSEP>[](symbol){key}<LSEP>[argument 2; litteral](str){ column in }<LSEP>[](symbol){name.df}<LSEP>[argument 4; litteral](str){ data frame.}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){after}<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){%in%}<LSEP>[](symbol){key}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){There is no }<LSEP>[](symbol){key}<LSEP>[argument 2; litteral](str){ column in }<LEND>[argument 3; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fh}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){, }<LEND>[argument 4; litteral](str){ data frame of }<LSEP>[](symbol){name.fh}<LSEP>[argument 6; litteral](str){.}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){fh.ret}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){df}<LEND>[](symbol){fh}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){keys}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){key}<LEND>[argument 1; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){fh}<LSEP>[argument 1; litteral](str){keys}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fh.ret}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){name.df}<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){%in%}<LSEP>[](symbol){key}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fh}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fh}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){There is no }<LSEP>[](symbol){key}<LSEP>[argument 2; litteral](str){ column in }<LEND>[argument 3; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fh}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fh}<LEND>[argument 1; litteral](str){, }<LEND>[argument 4; litteral](str){ data frame of }<LSEP>[](symbol){name.fh}<LSEP>[argument 6; litteral](str){.}<LEND>[statement 1; 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call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){fh.ret}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){createIndex}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){paths}<LSEP>[](symbol){base}<LSEP>[](symbol){dir}<LSEP>[](symbol){fname}<LSEP>[](symbol){meta}<LSEP>[](symbol){metadir}<LSEP>[](symbol){mname}<LSEP>[](symbol){gname}<LSEP>[](symbol){overwrite}<LSEP>[](symbol){checkwarn}<LSEP>[](symbol){checklog}<LSEP>[](symbol){quiet}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){compstart}<LEND>[call](){}<LSEP>[](symbol){Sys.time}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){messaget}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; 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){compstart}<LSEP>[argument 2; litteral](str){s}<LEND>[argument 3; litteral](str){ secs so far)}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){fileIndex}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){y/solar/}<LSEP>[argument 1; litteral](str){y/solar//}<LSEP>[](symbol){paths}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){fileIndex}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){multi_annual/}<LSEP>[argument 1; litteral](str){multi_annual//}<LSEP>[](symbol){fileIndex}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){fileIndex}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){subdaily/standard_format/}<LSEP>[argument 1; litteral](str){subdaily/standard_format//}<LSEP>[](symbol){fileIndex}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){fileIndex}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){^/}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){fileIndex}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){prec1min}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){substr}<LSEP>[](symbol){fileIndex}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){33.000000}<LEND>[argument 1; litteral](str){1_minute/precipitation/historical}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){prec1min}<LEND>[call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){substr}<LSEP>[](symbol){fileIndex}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){37.000000}<LEND>[argument 1; litteral](str){1_minute/precipitation/histori...}<LEND>[](symbol){prec1min}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){any1min}<LEND>[call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){prec1min}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){ncolumns}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){any1min}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){Splitting filenames...}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){fileIndex}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){l2df}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){pbapply}<LSEP>[](symbol){pblapply}<LEND>[](symbol){fileIndex}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){/}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){fileIndex}<LEND>[](symbol){ncolumns}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<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){in }<LSEP>[argument 2; litteral](str){: }<LEND>[argument 1; litteral](str){index does not have }<LSEP>[](symbol){ncolumns}<LSEP>[argument 3; litteral](str){ columns, but }<LEND>[argument 4; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){fileIndex}<LEND>[argument 5; litteral](logical){FALSE}<LEND>[statement 13; control flow](){if}<LSEP>[](symbol){any1min}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){prec1min}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){prec1min}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){fileIndex}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){res}<LSEP>[argument 1; litteral](str){var}<LSEP>[argument 2; litteral](str){per}<LSEP>[argument 3; 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call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){pbapply}<LSEP>[](symbol){pblapply}<LEND>[](symbol){file}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){[-_.]}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){id}<LSEP>[litteral](str){}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){per}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){per}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){sol}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){var}<LEND>[argument 1; litteral](str){solar}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){zip}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){info}<LSEP>[](symbol){}<LSEP>[argument 2; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){mirdwt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){yl}<LSEP>[](symbol){yh}<LSEP>[](symbol){h}<LSEP>[](symbol){L}<LEND>[body; block](){}<LSEP>[statement 0; call](){.Call}<LSEP>[call name; litteral](str){do_mirdwt}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){yl}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){yh}<LEND>[argument 2; call](){}<LSEP>[](symbol){as.vector}<LSEP>[](symbol){h}<LEND>[argument 3; call](){}<LSEP>[](symbol){as.integer}<LSEP>[](symbol){L}<LEND>[argument 4; litteral](str){rwt}

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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.keep.loc}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){loc.list}<LSEP>[](symbol){first}<LSEP>[](symbol){last}<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; 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litteral](str){to listed populations\n\n}<LEND>[statement 37; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clouds}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){pop}<LEND>[statement 38; 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){levels}<LSEP>[](symbol){p}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clouds}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clouds}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){pop}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LSEP>[](symbol){p}<LEND>[](symbol){i}<LEND>[](symbol){}<LEND>[statement 1; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){dct}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){variant}<LSEP>[](symbol){inverted}<LEND>[body; call](){}<LSEP>[](symbol){dtt}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){dct}<LSEP>[](symbol){variant}<LSEP>[](symbol){inverted}

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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){ttwa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){df}<LSEP>[](symbol){origin}<LSEP>[](symbol){destination}<LSEP>[](symbol){flow}<LSEP>[](symbol){conti}<LSEP>[](symbol){minimum_link}<LSEP>[](symbol){size_center}<LSEP>[](symbol){list_center}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){conti}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){origin}<LSEP>[](symbol){destination}<LSEP>[](symbol){flow}<LSEP>[](symbol){conti}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){origin}<LSEP>[argument 1; litteral](str){destination}<LSEP>[argument 2; 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[](){expression}<LSEP>[litteral](NULL){NULL}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.define.pop}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){ind.list}<LSEP>[](symbol){new}<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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litteral](logical){NA}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 42; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){prediction}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){prior.class}<LSEP>[argument 1; litteral](str){predicted.class}<LEND>[statement 43; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){prediction}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){prediction}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 44; assign](){<-}<LSEP>[](symbol){lev.class}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 45; assign](){<-}<LSEP>[variable; 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assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){distance}<LSEP>[](symbol){prediction}<LSEP>[](symbol){distances}<LEND>[argument 3; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){prox}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[statement 51; control flow](){if}<LSEP>[](symbol){misclass.ratio}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){confusion.mat}<LEND>[call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){prediction}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){class.ratio}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){confusion.mat}<LEND>[argument 1; call](){}<LSEP>[](symbol){rowSums}<LSEP>[](symbol){confusion.mat}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){class.ratio}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){class.ratio}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){misclassed}<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){prediction}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){prediction}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){prediction}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){results}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){confusion.mat}<LSEP>[](symbol){misclassed}<LEND>[statement 52; 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[](){expression}<LSEP>[litteral](str){metadata_example}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rt_ticket_attachments}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){ticket_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}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){rt_GET}<LSEP>[](symbol){url}<LSEP>[](symbol){...}<LEND>[statement 2; call](){}<LSEP>[](symbol){stopforstatus}<LSEP>[](symbol){out}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){location}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stringr}<LSEP>[](symbol){str_locate}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){out}<LSEP>[](symbol){body}<LEND>[argument 1; litteral](str){Attachments: }<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){location}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Error while processing respons...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){rest}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stringr}<LSEP>[](symbol){str_sub}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){out}<LSEP>[](symbol){body}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){location}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){nchar}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){out}<LSEP>[](symbol){body}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){attachments}<LEND>[call](){}<LSEP>[](symbol){parse_rt_properties}<LSEP>[](symbol){rest}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){attachments}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){attachment}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){props}<LEND>[call](){}<LSEP>[](symbol){as.list}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stringr}<LSEP>[](symbol){str_match}<LEND>[](symbol){attachment}<LSEP>[argument 1; litteral](str){\\(?(.+)\\) \\((.+) \\/ (.+)\\)}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){props}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Name}<LSEP>[argument 1; litteral](str){Type}<LSEP>[argument 2; litteral](str){Size}<LEND>[](symbol){props}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){result}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){try_tibble}<LEND>[argument 0; call](){}<LSEP>[](symbol){data.frame}<LEND>[statement 9; call](){}<LSEP>[](symbol){try_tibble}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){result}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){do.call}<LSEP>[](symbol){rbind}<LEND>[argument 1; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){result}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){FALSE}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){kurtosis.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){na.rm}<LSEP>[](symbol){type}<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){fold}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fold}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){jnum}<LEND>[call](){}<LSEP>[](symbol){logical}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){j}<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>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){jnum}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){is.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){notnum}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){jnum}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){notnum}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){There are omitted variables (n...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){notnum}<LSEP>[argument 1; litteral](str){ }<LEND>[argument 2; litteral](str){}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){fold.num}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[argument 0; litteral](str){list}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fold}<LEND>[statement 8; 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){fold.num}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fold.num}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fold}<LSEP>[](symbol){n}<LEND>[](symbol){jnum}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fold.num}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fold}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){fold.num}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){kurtosis}<LSEP>[](symbol){na.rm}<LSEP>[](symbol){type}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl2treemix}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){outfile}<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){outfile}<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){$}<LEND>[argument 0; 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control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\nRaw Fixed Difference Matrix\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd2}<LSEP>[](symbol){fd}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<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){Sample sizes}<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 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd2}<LSEP>[](symbol){gl}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd2}<LSEP>[](symbol){fd}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd2}<LSEP>[](symbol){pcfd}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd2}<LSEP>[](symbol){nobs}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd2}<LSEP>[](symbol){nloc}<LEND>[argument 5; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd2}<LSEP>[](symbol){expfpos}<LEND>[argument 6; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd2}<LSEP>[](symbol){sdfpos}<LEND>[argument 7; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd2}<LSEP>[](symbol){pval}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){l}<LEND>[litteral](str){fd}<LEND>[statement 22; 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 of class 'fd'...}<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 -- NAs...}<LSEP>[argument 7; litteral](str){ [[7]] $sdfpos -- NAs,...}<LSEP>[argument 8; litteral](str){ [[8]] $prob -- NAs, p...}<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){l}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.filter.locmetric}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){metric}<LSEP>[](symbol){upper}<LSEP>[](symbol){lower}<LSEP>[](symbol){keep}<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; 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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 8; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){gl.filter.monomorphs}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 9; 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 10; 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 11; 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){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){metric}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){keep}<LSEP>[argument 1; litteral](str){within}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){}<LSEP>[](symbol){field}<LEND>[](symbol){lower}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){}<LSEP>[](symbol){field}<LEND>[](symbol){upper}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){index}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x2}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){index}<LSEP>[](symbol){}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){keep}<LSEP>[argument 1; litteral](str){outside}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){}<LSEP>[](symbol){field}<LEND>[](symbol){lower}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){}<LSEP>[](symbol){field}<LEND>[](symbol){upper}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){index}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x2}<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>[](symbol){index}<LSEP>[](symbol){}<LEND>[statement 14; 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){ Initial number of loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; 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litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<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){x2}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){metaInfo}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){id}<LSEP>[](symbol){hasfileonly}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){id}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){id}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sel}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){metaIndex}<LSEP>[](symbol){Stations_id}<LEND>[](symbol){id}<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){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){rdwd::metaIndex contains no en...}<LSEP>[](symbol){id}<LSEP>[argument 2; litteral](str){. This ID probably does not ex...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nonpubmes}<LSEP>[litteral](str){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){nonpub}<LEND>[call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){metaIndex}<LSEP>[](symbol){sel}<LSEP>[argument 2; litteral](str){hasfile}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){nonpub}<LEND>[](symbol){hasfileonly}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){nonpubmes}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){\nAdditionally, there are }<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){nonpub}<LEND>[argument 2; litteral](str){ non-public files. 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