Search is not available for this dataset
ast
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ment 2; litteral](str){x2}<LSEP>[argument 3; litteral](str){y2}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){ggplot}<LSEP>[](symbol){coorij}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes_q}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){y1}<LEND>[argument 2; call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){x2}<LEND>[argument 3; call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){y2}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){graph}<LEN
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}<LSEP>[argument 1; litteral](str){inches}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){graph}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){graph}<LEND>[argument 1; call](){}<LSEP>[](symbol){labs}<LSEP>[](symbol){main}<LSEP>[](symbol){sub.title}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){coor}<LEND>[](symbol){i1}<LEND>[argument 1; litteral](str){ (}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){inertia}<LSEP>[](symbol){i1}<LEND>[argument 3; litteral](str){%)}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP
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LEND>[statement 5; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){graph}<LEND>[statement 10; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](NULL){NULL}
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unname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](sy
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tement 9; assign](){<-}<LSEP>[](symbol){hold.nInd}<LEND>[call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){hold.nPop}<LEND>[call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Extracting current individual ...}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){recode.table}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){indNames}<LSEP>[](
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ment 17; assign](){<-}<LSEP>[](symbol){ntr}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){new}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 18; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){ntr}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbo
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n](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.filter.monomorphs}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n Summary of recoded dataset\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Original No. of loci:}<LSEP>[](symbol){hold.nLoc}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){pas
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P>[argument 0; litteral](str){ Original No. of populations:}<LSEP>[](symbol){hold.nPop}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ New No. of populations:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n\n}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){recalc}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Note: Locus metrics not recalc...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){mono.rm}<LEND
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call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol)
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SEP>[](symbol){match.call}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 28; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}
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(real){2.000000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){l}<LSEP>[litteral](real){3.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Testing Results\n}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){k}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nAccuracy:}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>
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bol){l}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){l}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\n}
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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](){}
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SEP>[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){1.00000
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){}<LSEP>[](symbol){length}<LSEP>[](symbol){ind.list}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: no individuals ...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Deleteing all but the list...}<LSEP>[](symbol){ind.list}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%
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l){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[]
|
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argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symb
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[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str
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tr){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call]
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ll](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence ...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral]
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0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){TrimmedSequence}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Data must include...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>
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l){cat}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'threshol...}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){threshold}<LSEP>[litteral](real){0.200000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Note: Hamming distance range...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Note: Calculating pairwise H...}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[
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