Datasets:
lanesket
/
r-asts-tokenized

Dataset card Data Studio Files Community
ast
stringlengths
16
28.2M
input_ids
list
attention_mask
list
labels
list
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){ddjeffreyspar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){p1}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){p2}<LEND>[](symbol){k}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p1 and p2 must have the same n...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){p2}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){p1 and p2 must be vectors with...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){dd}<LEND>[litteral](logical){NA}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){dd}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){p2}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){p1}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){p2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){dd}<LEND>[litteral](logical){NA}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){dd}<LSEP>[argument 1; litteral](logical){TRUE}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){useDplyr}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; assign](){<-}<LSEP>[](symbol){useDplyr}<LEND>[call](){}<LSEP>[](symbol){getOption}<LSEP>[argument 0; litteral](str){dat.use.dplyr}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){requireNamespace}<LSEP>[argument 0; litteral](str){dplyr}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){option('dat.use.dplyr') is set...}<LSEP>[argument 1; litteral](str){not be loaded. Set option to F...}<LSEP>[argument 2; litteral](str){dplyr.)}<LEND>[](symbol){useDplyr}<LEND>[assign](){<-}<LSEP>[](symbol){.onAttach}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){libname}<LSEP>[](symbol){pkgname}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){packageStartupMessage}<LSEP>[argument 0; litteral](str){To use dplyr as backend set 'o...}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){getcol.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){name}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){object}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){getcol.folder applies to an ob...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){[}<LSEP>[](symbol){name}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){object}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){xf}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){create_dat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dir}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){system}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){dat create %s}<LSEP>[](symbol){dir}<LEND>[assign](){<-}<LSEP>[](symbol){share_dat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dir}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){system}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){dat share %s}<LSEP>[](symbol){dir}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[assign](){<-}<LSEP>[](symbol){clone_dat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){link}<LSEP>[](symbol){dir}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){dir.exists}<LSEP>[](symbol){dir}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){dir.create}<LSEP>[](symbol){dir}<LEND>[statement 1; call](){}<LSEP>[](symbol){system}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){dat clone %s %s}<LSEP>[](symbol){link}<LSEP>[](symbol){dir}<LEND>[assign](){<-}<LSEP>[](symbol){pull_dat}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){system}<LSEP>[argument 0; litteral](str){dat pull}<LEND>[assign](){<-}<LSEP>[](symbol){sync_dat}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){system}<LSEP>[argument 0; litteral](str){dat sync}<LEND>[assign](){<-}<LSEP>[](symbol){log_dat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){path}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){system}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){dat log %s}<LSEP>[](symbol){path}<LEND>[assign](){<-}<LSEP>[](symbol){status_dat}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){system}<LSEP>[argument 0; litteral](str){dat status}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.plot.heatmap}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){D}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pkg}<LSEP>[litteral](str){RColorBrewer}<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){pkg}<LSEP>[litteral](str){pheatmap}<LEND>[statement 3; 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 4; 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 5; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 7; 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 8; 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 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){class}<LSEP>[](symbol){D}<LEND>[argument 1; litteral](str){dist}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){D}<LEND>[argument 1; litteral](str){matrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){D}<LEND>[argument 1; litteral](str){fd}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Fatal Error: distance matrix...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){D}<LEND>[argument 1; litteral](str){dist}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){D}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: matrix contains n...}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){D}<LEND>[argument 1; litteral](str){fd}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){D}<LSEP>[](symbol){fd}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: matrix contains n...}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){D}<LEND>[argument 1; litteral](str){dist}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){pheatmap}<LSEP>[](symbol){pheatmap}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){D}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RColorBrewer}<LSEP>[](symbol){brewer.pal}<LEND>[argument 0; litteral](real){8.000000}<LSEP>[argument 1; litteral](str){Blues}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){D}<LEND>[argument 1; litteral](str){fd}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){pheatmap}<LSEP>[](symbol){pheatmap}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){D}<LSEP>[](symbol){fd}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RColorBrewer}<LSEP>[](symbol){brewer.pal}<LEND>[argument 0; litteral](real){8.000000}<LSEP>[argument 1; litteral](str){Blues}<LEND>[statement 14; 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 15; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](NULL){NULL}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){stopforstatus}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){response}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){status}<LEND>[argument 1; litteral](real){400.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){message}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matjeffreyspar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){meanL}<LSEP>[](symbol){varL}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){meanL}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){meanL}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){meanL}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){meanL}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){jeffreyspar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){meanL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){meanL}<LSEP>[](symbol){j}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){j}<LEND>[statement 3; call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){distances}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matdistl2dnorm}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){method}<LSEP>[](symbol){varwL}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){matdistl2d now applies to an o...}<LEND>[statement 1; 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 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){is.numeric}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Non numeric column(s) in the d...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){n}<LEND>[statement 5; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){matipl2d}<LSEP>[](symbol){x}<LSEP>[](symbol){method}<LSEP>[](symbol){varwL}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){norme}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){W}<LEND>[statement 8; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n}<LEND>[body; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){norme}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){norme}<LSEP>[](symbol){j}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 10; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[statement 11; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n}<LEND>[body; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[statement 12; call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){distances}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){hclustdd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){xf}<LSEP>[](symbol){group.name}<LSEP>[](symbol){distance}<LSEP>[](symbol){sub.title}<LSEP>[](symbol){filename}<LSEP>[](symbol){method.hclust}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){xf}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){xf}<LEND>[argument 1; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){xf}<LSEP>[](symbol){is.array}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){hclustdd applies to a data fra...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){xf}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){xf}<LSEP>[](symbol){group.name}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[litteral](str){group}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){group}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nb.groups}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LSEP>[](symbol){group}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){groups.name}<LEND>[call](){}<LSEP>[](symbol){levels}<LSEP>[](symbol){group}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){vars.name}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){print.ata}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Assemble}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){form_map}<LEND>[argument 2; litteral](str){forms from}<LEND>[argument 3; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){groups}<LEND>[argument 4; litteral](str){items.\n}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){items}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){The ATA problem hasn't been so...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){The ATA problem has been solve...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){status}<LEND>[argument 1; litteral](str){, optimum: }<LEND>[argument 2; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){optimum}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 3; litteral](str){ (}<LEND>[argument 4; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){obj_vars}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](str){, }<LEND>[argument 5; litteral](str){)\n}<LSEP>[argument 6; litteral](str){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){items}<LEND>[call](){}<LSEP>[](symbol){ata_extract_items}<LSEP>[](symbol){x}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){items}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){items}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){items}<LEND>[call](){}<LSEP>[](symbol){ata_results_to_model}<LSEP>[](symbol){items}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){items}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){items}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){items}<LEND>[call](){}<LSEP>[](symbol){ata_results_to_dataframe}<LSEP>[](symbol){items}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){items}<LEND>[argument 1; litteral](real){10.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){items}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){items}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[](symbol){}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){...\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){items}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){4.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){items}<LEND>[](symbol){}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){See more results in 'x$items' ...}<LEND>[statement 2; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){plot.ata}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ata}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Not an 'ata' object}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){items}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The ATA problem hasn't been so...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){opts}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){opts}<LSEP>[](symbol){theta}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){opts}<LSEP>[](symbol){theta}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){3.000000}<LEND>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){0.100000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){n_thetas}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){opts}<LSEP>[](symbol){theta}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){n_forms}<LEND>[call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){form_map}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){items}<LEND>[call](){}<LSEP>[](symbol){ata_extract_items}<LSEP>[](symbol){x}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){info}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){items}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){xx}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){model_mixed_info}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){opts}<LSEP>[](symbol){theta}<LEND>[](symbol){xx}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){opts}<LEND>[](symbol){D}<LEND>[statement 1; call](){}<LSEP>[](symbol){rowSums}<LSEP>[](symbol){xx}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){info}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Form}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n_forms}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){info}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){opts}<LSEP>[](symbol){theta}<LEND>[](symbol){info}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){info}<LEND>[call](){}<LSEP>[](symbol){melt}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){info}<LEND>[argument 1; litteral](str){t}<LSEP>[argument 2; litteral](str){Forms}<LEND>[statement 11; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ggplot}<LSEP>[](symbol){info}<LEND>[argument 1; call](){}<LSEP>[](symbol){aes_string}<LSEP>[argument 0; litteral](str){t}<LSEP>[argument 1; litteral](str){value}<LSEP>[argument 2; litteral](str){Forms}<LEND>[argument 1; call](){}<LSEP>[](symbol){geom_line}<LEND>[argument 1; call](){}<LSEP>[](symbol){xlab}<LEND>[argument 0; call](){}<LSEP>[](symbol){expression}<LSEP>[](symbol){theta}<LEND>[argument 1; call](){}<LSEP>[](symbol){ylab}<LSEP>[argument 0; litteral](str){Test Information}<LEND>[argument 1; call](){}<LSEP>[](symbol){theme_bw}<LEND>[argument 1; call](){}<LSEP>[](symbol){theme}<LEND>[argument 0; call](){}<LSEP>[](symbol){element_blank}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plot.drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dotargs}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){named}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){dotargs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){rep_len}<LSEP>[argument 0; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dotargs}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){dotargs}<LEND>[argument 1; litteral](str){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){fit_objects}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dotargs}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){named}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){is_drda}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){fit_objects}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){drda}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){fit_objects}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fit_objects}<LSEP>[](symbol){is_drda}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fit_objects}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){plot.drdalist}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){x}<LEND>[](symbol){fit_objects}<LEND>[](symbol){...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){col}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){col}<LEND>[statement 7; 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assign](){<-}<LSEP>[](symbol){yci}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){upper_bound}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){i}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cc}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){col2rgb}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){col}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){255.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){cc}<LEND>[call](){}<LSEP>[](symbol){rgb}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cc}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cc}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 3; litteral](real){0.080000}<LEND>[statement 4; call](){}<LSEP>[](symbol){polygon}<LSEP>[](symbol){xci}<LSEP>[](symbol){yci}<LSEP>[](symbol){cc}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){mean_fn}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){mean_function}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){phi}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mean_fn}<LSEP>[argument 1; litteral](str){logistic4}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){coefficients}<LEND>[argument 1; litteral](real){4.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){mean_fn}<LSEP>[argument 1; litteral](str){logistic2}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){coefficients}<LEND>[argument 1; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](real){nan}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){phi}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){fn}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){phi}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){coefficients}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){e}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){phi}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){phi}<LSEP>[](symbol){k}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){phi}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){phi}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){phi}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){usr}<LEND>[argument 1; litteral](real){3.000000}<LEND>[](symbol){f}<LEND>[argument 2; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){col}<LSEP>[](symbol){i}<LEND>[statement 1; call](){}<LSEP>[](symbol){lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){usr}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){phi}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){f}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](real){3.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){col}<LSEP>[](symbol){i}<LEND>[statement 41; assign](){<-}<LSEP>[](symbol){location}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){eta}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){bottomleft}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){topleft}<LEND>[statement 42; assign](){<-}<LSEP>[](symbol){legend_labels}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){legend}<LEND>[statement 43; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){legend_labels}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){legend_labels}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){y}<LSEP>[](symbol){mean_function}<LEND>[argument 2; litteral](str){a}<LEND>[statement 44; call](){}<LSEP>[](symbol){legend}<LSEP>[](symbol){location}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){col}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M}<LEND>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](str){white}<LSEP>[](symbol){legend_labels}<LEND>[statement 45; call](){}<LSEP>[](symbol){dev.flush}<LEND>[statement 46; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](NULL){NULL}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plot.ata}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){conditem}<LSEP>[](symbol){useconst}<LSEP>[](symbol){itemorder}<LSEP>[](symbol){itemlab}<LSEP>[](symbol){useitemlab}<LSEP>[](symbol){together}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){oldpar}<LEND>[call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 1; call](){}<LSEP>[](symbol){on.exit}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){oldpar}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){names_const}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){plotconst}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){useconst}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[](symbol){names_const}<LEND>[false branch; block](){}<LSEP>[](symbol){useconst}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){nC}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){names_const}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){plotnC}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){plotconst}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){nI}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){itemorder}<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){itemorder}<LEND>[](symbol){nI}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Provided item order is shorter...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){itemorder}<LEND>[](symbol){nI}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Provided item order longer tha...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; 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call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<LSEP>[](symbol){useorder}<LEND>[argument 3; litteral](real){0.800000}<LEND>[statement 18; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){cumulative}
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litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 18; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}
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[](){expression}<LSEP>[litteral](NULL){NULL}<LEND>[assign](){<-}<LSEP>[](symbol){dtwpairdist}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){dtw}<LSEP>[argument 0; litteral](logical){TRUE}<LSEP>[](symbol){...}<LEND>[](symbol){distance}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){DRAT_ARCHIVE_SUB_DIR}<LSEP>[litteral](str){Archive}<LEND>[assign](){<-}<LSEP>[](symbol){DRAT_BINARY_TYPES}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){mac.binary}<LSEP>[argument 1; litteral](str){mac.binary.el-capitan}<LSEP>[argument 2; litteral](str){mac.binary.mavericks}<LSEP>[argument 3; litteral](str){win.binary}<LEND>[assign](){<-}<LSEP>[](symbol){DRAT_BOTH_TYPES}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){source}<LSEP>[argument 1; litteral](str){mac.binary}<LSEP>[argument 2; litteral](str){mac.binary.el-capitan}<LSEP>[argument 3; litteral](str){mac.binary.mavericks}<LSEP>[argument 4; litteral](str){win.binary}<LEND>[assign](){<-}<LSEP>[](symbol){DRAT_VERSION_REGEX}<LSEP>[litteral](str){[0-9]\\.[0-9]$}<LEND>[assign](){<-}<LSEP>[](symbol){DRAT_CONTRIB_VERSION_REGEX}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){contrib/}<LSEP>[](symbol){DRAT_VERSION_REGEX}<LEND>[assign](){<-}<LSEP>[](symbol){.check_path}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){repopath}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){dir.exists}<LSEP>[](symbol){repopath}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Directory '}<LSEP>[](symbol){repopath}<LSEP>[argument 2; litteral](str){' does not exist or cannot be ...}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[assign](){<-}<LSEP>[](symbol){.norm_type}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){type}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){type}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){source}<LSEP>[argument 1; litteral](str){binary}<LSEP>[argument 2; litteral](str){mac.binary}<LSEP>[argument 3; litteral](str){mac.binary.el-capitan}<LSEP>[argument 4; litteral](str){mac.binary.mavericks}<LSEP>[argument 5; litteral](str){win.binary}<LSEP>[argument 6; litteral](str){both}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){both}<LSEP>[](symbol){type}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){DRAT_BOTH_TYPES}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){binary}<LSEP>[](symbol){type}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){type}<LSEP>[](symbol){DRAT_BINARY_TYPES}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){type}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){binary}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){type}<LEND>[](symbol){type}<LEND>[assign](){<-}<LSEP>[](symbol){.norm_pkg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){pkg}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){pkg}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pkg}<LSEP>[litteral](NULL){NULL}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pkg}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){pkg}<LEND>[](symbol){pkg}<LEND>[assign](){<-}<LSEP>[](symbol){.check_location_arg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){location}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LSEP>[](symbol){location}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){gh-pages}<LSEP>[argument 1; litteral](str){docs}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The 'location' argument '}<LSEP>[](symbol){location}<LSEP>[argument 2; litteral](str){' is unsuitable.}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[litteral](NULL){NULL}<LEND>[assign](){<-}<LSEP>[](symbol){archivePackages}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){repopath}<LSEP>[](symbol){type}<LSEP>[](symbol){pkg}<LSEP>[](symbol){version}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){.check_path}<LSEP>[](symbol){repopath}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){.norm_type}<LSEP>[](symbol){type}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){pkg}<LEND>[call](){}<LSEP>[](symbol){.norm_pkg}<LSEP>[](symbol){pkg}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){repoinfo}<LEND>[call](){}<LSEP>[](symbol){getRepoInfo}<LSEP>[](symbol){repopath}<LSEP>[](symbol){type}<LSEP>[](symbol){pkg}<LSEP>[](symbol){version}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){repoinfo}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){repoinfo}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){repoinfo}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){newest}<LEND>[](symbol){}<LEND>[statement 5; call](){}<LSEP>[](symbol){.prepare_archive_directory}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repoinfo}<LSEP>[](symbol){contrib.url}<LEND>[statement 6; call](){}<LSEP>[](symbol){mapply}<LSEP>[](symbol){.make_archive_directory}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repoinfo}<LSEP>[](symbol){contrib.url}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repoinfo}<LSEP>[](symbol){package}<LEND>[statement 7; call](){}<LSEP>[](symbol){mapply}<LSEP>[](symbol){.move_to_archive_directory}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repoinfo}<LSEP>[](symbol){contrib.url}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repoinfo}<LSEP>[](symbol){package}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repoinfo}<LSEP>[](symbol){file}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){repoinfo}<LEND>[argument 1; litteral](integer){1}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){updateRepo}<LSEP>[](symbol){repopath}<LEND>[argument 1; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repoinfo}<LSEP>[](symbol){type}<LEND>[](symbol){version}<LEND>[statement 9; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](NULL){NULL}<LEND>[assign](){<-}<LSEP>[](symbol){.prepare_archive_directory}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){repodir}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){archive}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){repodir}<LSEP>[](symbol){DRAT_ARCHIVE_SUB_DIR}<LEND>[argument 1; call](){}<LSEP>[](symbol){file.exists}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){repodir}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){archive_exits}<LEND>[call](){}<LSEP>[](symbol){file.exists}<LSEP>[](symbol){archive}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){archive_exits}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){archive}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){archive}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){archive_exits}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){archive_created}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){archive}<LSEP>[](symbol){dir.create}<LEND>[argument 2; call](){}<LSEP>[](symbol){logical}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 3; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){archive_created}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Archive directory not found an...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[assign](){<-}<LSEP>[](symbol){.make_archive_directory}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rd}<LSEP>[](symbol){pkg}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parchive}<LEND>[call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){rd}<LSEP>[](symbol){DRAT_ARCHIVE_SUB_DIR}<LSEP>[](symbol){pkg}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.exists}<LSEP>[](symbol){parchive}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){dir.create}<LSEP>[](symbol){parchive}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Package archive directory for }<LSEP>[](symbol){pkg}<LSEP>[argument 2; litteral](str){ not found and couldn't be cre...}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[](symbol){parchive}<LEND>[assign](){<-}<LSEP>[](symbol){.move_to_archive_directory}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rd}<LSEP>[](symbol){pkg}<LSEP>[](symbol){file}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){file.rename}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){rd}<LSEP>[](symbol){file}<LEND>[argument 1; call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){rd}<LSEP>[](symbol){DRAT_ARCHIVE_SUB_DIR}<LSEP>[](symbol){pkg}<LSEP>[](symbol){file}<LEND>[assign](){<-}<LSEP>[](symbol){archivePackagesForAllRversions}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){repopath}<LSEP>[](symbol){type}<LSEP>[](symbol){pkg}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){archivePackages}<LSEP>[](symbol){repopath}<LSEP>[](symbol){type}<LSEP>[](symbol){pkg}<LSEP>[argument 3; litteral](logical){NA}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){discdd.misclass}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){xf}<LSEP>[](symbol){class.var}<LSEP>[](symbol){distance}<LSEP>[](symbol){crit}<LSEP>[](symbol){p}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){xf}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){discdd.misclass applies to a f...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folderh}<LSEP>[](symbol){xf}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){xf}<LSEP>[](symbol){is.array}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){discdd.misclass applies to a f...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){class.var}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){class.var}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){If xf is a list of arrays, cla...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){crit}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){crit must be 1 or 2.}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){distance}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){distance}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.folderh}<LSEP>[](symbol){xf}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){xf}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){discdd.misclass applies to a f...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xf}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){The 1st data frame of xf must ...}<LEND>[statement 2; 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call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){misclass}<LSEP>[](symbol){misclassed}<LEND>[](symbol){distances}<LEND>[argument 6; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){prox}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){results}<LEND>[litteral](str){discdd.misclass}<LEND>[statement 24; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){results}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){utils.recalc.freqhomsnp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){hold}<LSEP>[](symbol){x}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Fatal Error: genlight object...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 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){stop}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Dataset contains mo...}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){ calculations\n}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){FreqHomSnp}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){FreqHomSnp}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Locus metric FreqHomSnp does...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Recalculating locus metric f...}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){FreqHomSnp}<LEND>[call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){T}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){FreqHomSnp}<LEND>[litteral](logical){TRUE}<LEND>[statement 14; 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 15; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){ddlp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LSEP>[](symbol){p}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){x1}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){x1}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){x2}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){x2}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x1}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){x1 must be a data frame or a v...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x2}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){x2 must be a data frame or a v...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x1}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x2}<LEND>[](symbol){k}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ncol(x1) != ncol(x2)}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x2}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){x1 and x2 do not have the same...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x1}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x2}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 9; 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){x1}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lev}<LEND>[call](){}<LSEP>[](symbol){union}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[](symbol){lev}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[](symbol){lev}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){p1}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x1}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){p2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){x2}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x2}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){ddlppar}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}<LSEP>[](symbol){p}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){mathellinger}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){x must be an object of class '...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){is.numeric}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Non numeric column(s) in the d...}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[body; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){hellinger}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){j}<LEND>[statement 5; call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){distances}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){formula}<LSEP>[](symbol){data}<LSEP>[](symbol){subset}<LSEP>[](symbol){weights}<LSEP>[](symbol){na.action}<LSEP>[](symbol){mean_function}<LSEP>[](symbol){is_log}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){upper_bound}<LSEP>[](symbol){start}<LSEP>[](symbol){max_iter}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){model_frame}<LEND>[call](){}<LSEP>[](symbol){match.call}<LSEP>[argument 0; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){arg_name}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){model_frame}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){arg_idx}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){formula}<LSEP>[argument 1; litteral](str){data}<LSEP>[argument 2; litteral](str){subset}<LSEP>[argument 3; litteral](str){weights}<LSEP>[argument 4; litteral](str){na.action}<LEND>[](symbol){arg_name}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){model_frame}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){model_frame}<LSEP>[](symbol){arg_idx}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){model_frame}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){quote}<LSEP>[](symbol){model.frame}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){model_frame}<LEND>[call](){}<LSEP>[](symbol){eval}<LSEP>[](symbol){model_frame}<LEND>[argument 1; call](){}<LSEP>[](symbol){parent.frame}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){model_terms}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){model_frame}<LSEP>[argument 1; litteral](str){terms}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){model_matrix}<LEND>[call](){}<LSEP>[](symbol){model.matrix}<LSEP>[](symbol){model_terms}<LSEP>[](symbol){model_frame}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){model_matrix}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){model_matrix}<LSEP>[argument 1; litteral](str){assign}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 3; litteral](logical){TRUE}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){0 (non-NA) cases}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){model.response}<LSEP>[](symbol){model_frame}<LSEP>[argument 1; litteral](str){numeric}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){y}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){response variable must be a ve...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[](symbol){n}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){incompatible dimensions}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){model.weights}<LSEP>[](symbol){model_frame}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){w}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){w}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'weights' must be a numeric ve...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){w}<LEND>[](symbol){n}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){incompatible dimensions}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){w}<LSEP>[argument 1; 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call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nOptimization algorithm DID N...}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){iterations}<LEND>[argument 2; litteral](str){iterations\n}<LEND>[statement 14; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){residuals.drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){type}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){residuals}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){type}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){response}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){weights}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){weights}<LEND>[](symbol){r}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){pearson}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){r}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){r}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){sigma}<LEND>[statement 3; call](){}<LSEP>[](symbol){naresid}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){na.action}<LEND>[](symbol){r}<LEND>[assign](){<-}<LSEP>[](symbol){sigma.drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){sigma}<LEND>[assign](){<-}<LSEP>[](symbol){summary.drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){std_err}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){vcov}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){pearson_resid}<LEND>[call](){}<LSEP>[](symbol){residuals}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){pearson}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){sigma}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){logistic2_fit}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Growth rate}<LSEP>[argument 1; litteral](str){Midpoint at}<LSEP>[argument 2; litteral](str){Residual std err.}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){logistic4_fit}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Minimum}<LSEP>[argument 1; litteral](str){Maximum}<LSEP>[argument 2; litteral](str){Growth rate}<LSEP>[argument 3; litteral](str){Midpoint at}<LSEP>[argument 4; litteral](str){Residual std err.}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LSEP>[argument 0; litteral](real){0.025000}<LEND>[](symbol){std_err}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){qnorm}<LSEP>[argument 0; litteral](real){0.975000}<LEND>[](symbol){std_err}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Estimate}<LSEP>[argument 1; litteral](str){Lower .95}<LSEP>[argument 2; litteral](str){Upper .95}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){is_log}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){logistic2_fit}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){}<LEND>[call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){logistic4_fit}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[argument 1; litteral](real){4.000000}<LSEP>[](symbol){}<LEND>[call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){param}<LEND>[argument 1; litteral](real){4.000000}<LSEP>[](symbol){}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){estimated}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){aic}<LEND>[call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){loglik}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){bic}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){n}<LEND>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){loglik}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){object}<LEND>[litteral](str){summary.drda}<LEND>[](symbol){object}<LEND>[assign](){<-}<LSEP>[](symbol){weights.drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){na.action}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){weights}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){naresid}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){na.action}<LEND>[argument 1; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl2phylip}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){outfile}<LSEP>[](symbol){outpath}<LSEP>[](symbol){bstrap}<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){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Fatal Error: genlight object...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Population assignments not d...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](str){pop1}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 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){>=}<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){Converting to a matrix of freq...}<LEND>[statement 11; assign](){=}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){tapply}<LEND>[argument 3; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){e}<LEND>[body; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){e}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Computing Euclidean distances\n}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){dist}<LSEP>[](symbol){t}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){d}<LEND>[argument 1; litteral](str){ }<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){substr}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){d}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){10.000000}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Writing the Phylip input file}<LSEP>[](symbol){outfilespec}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){bstrap}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Repeating calculations for}<LSEP>[](symbol){bstrap}<LSEP>[argument 2; litteral](str){iterations\n}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){npops}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 18; call](){}<LSEP>[](symbol){sink}<LSEP>[](symbol){outfilespec}<LEND>[statement 19; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){ }<LSEP>[](symbol){npops}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 20; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){npops}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){d}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){d}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){bstrap}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){bstrap}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){h}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){newx}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){sample}<LSEP>[](symbol){h}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){newx}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){tapply}<LEND>[argument 3; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){e}<LEND>[body; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){e}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){dist}<LSEP>[](symbol){t}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){d}<LEND>[argument 1; litteral](str){ }<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){substr}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){d}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){10.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){npops}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 7; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){ }<LSEP>[](symbol){npops}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 8; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){npops}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){d}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){d}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 22; call](){}<LSEP>[](symbol){sink}<LEND>[statement 23; 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){Closing output file}<LSEP>[](symbol){outfile}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 24; 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 25; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){d}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.refindicesurl}<LSEP>[litteral](str){https://api.twelvedata.com/ind...}<LEND>[assign](){<-}<LSEP>[](symbol){ref_indices}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){sym}<LSEP>[](symbol){as}<LSEP>[](symbol){country}<LSEP>[](symbol){apikey}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){apikey}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){apikey}<LEND>[call](){}<LSEP>[](symbol){.get_apikey}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){as}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){as}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){.refindicesurl}<LSEP>[argument 1; litteral](str){?}<LSEP>[argument 2; litteral](str){&apikey=}<LSEP>[](symbol){apikey}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sym}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&symbol=}<LSEP>[](symbol){sym}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){country}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&country=}<LSEP>[](symbol){country}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){accessed}<LEND>[call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[argument 1; litteral](str){UTC}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RcppSimdJson}<LSEP>[](symbol){fload}<LEND>[](symbol){qry}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){as}<LSEP>[argument 1; litteral](str){raw}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){qry}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){res}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){res}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){res}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){status}<LEND>[argument 1; litteral](str){ok}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){message}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){data}<LEND>[](symbol){dat}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[argument 0; litteral](str){rbind}<LSEP>[](symbol){dat}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){dat}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){API returned NULL data. Try to...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dat}<LSEP>[argument 1; litteral](str){accessed}<LEND>[](symbol){accessed}<LEND>[](symbol){dat}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){print.fhclustd}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){dist.print}<LSEP>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){dist.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){distances between groups\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){distances}<LEND>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){clust}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){suff_stats}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){w}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){unique_x}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){unique_x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){stats}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){nan}<LSEP>[](symbol){k}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){stats}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){x}<LSEP>[argument 1; litteral](str){n}<LSEP>[argument 2; litteral](str){m}<LSEP>[argument 3; litteral](str){v}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){k}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){idx}<LEND>[call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){unique_x}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){idx}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LSEP>[](symbol){idx}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){q}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LSEP>[](symbol){z}<LEND>[](symbol){t}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){v}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){z}<LSEP>[](symbol){m}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){t}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){unique_x}<LSEP>[](symbol){i}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){t}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[](symbol){m}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){stats}<LSEP>[](symbol){i}<LSEP>[argument 2; 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[](){expression}<LSEP>[litteral](NULL){NULL}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.refcryptopairsurl}<LSEP>[litteral](str){https://api.twelvedata.com/cry...}<LEND>[assign](){<-}<LSEP>[](symbol){ref_crypto_pairs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){sym}<LSEP>[](symbol){as}<LSEP>[](symbol){exchange}<LSEP>[](symbol){currency_base}<LSEP>[](symbol){currency_quote}<LSEP>[](symbol){flatten_exchanges}<LSEP>[](symbol){apikey}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){apikey}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){apikey}<LEND>[call](){}<LSEP>[](symbol){.get_apikey}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){as}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){as}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){.refcryptopairsurl}<LSEP>[argument 1; litteral](str){?}<LSEP>[argument 2; litteral](str){&apikey=}<LSEP>[](symbol){apikey}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sym}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&symbol=}<LSEP>[](symbol){sym}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){exchange}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&exchange=}<LSEP>[](symbol){exchange}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){currency_base}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&currency_base=}<LSEP>[](symbol){currency_base}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){currency_quote}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&currency_quote=}<LSEP>[](symbol){currency_quote}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){accessed}<LEND>[call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[argument 1; litteral](str){UTC}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RcppSimdJson}<LSEP>[](symbol){fload}<LEND>[](symbol){qry}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){as}<LSEP>[argument 1; litteral](str){raw}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){qry}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){res}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){res}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){res}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){status}<LEND>[argument 1; litteral](str){ok}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){message}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){data}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){A query returned NULL data.}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){data}<LEND>[](symbol){dat}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[argument 0; litteral](str){rbind}<LSEP>[](symbol){dat}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){dat}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The API returned NULL data. Tr...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 15; control flow](){if}<LSEP>[](symbol){flatten_exchanges}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq_along}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dat}<LSEP>[](symbol){symbol}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dat}<LSEP>[](symbol){symbol}<LEND>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dat}<LSEP>[](symbol){available_exchanges}<LEND>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dat}<LSEP>[](symbol){currency_base}<LEND>[](symbol){x}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dat}<LSEP>[](symbol){currency_quote}<LEND>[](symbol){x}<LEND>[argument 4; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[argument 0; litteral](str){rbind}<LSEP>[](symbol){dat}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dat}<LSEP>[argument 1; litteral](str){accessed}<LEND>[](symbol){accessed}<LEND>[](symbol){dat}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){wasserstein}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LSEP>[](symbol){check}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){NCOL}<LSEP>[](symbol){x1}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){NCOL}<LSEP>[](symbol){x2}<LEND>[](symbol){p}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){x1 and x2 must be two vectors,...}<LEND>[statement 2; 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>[condition; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x1}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x2}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){x1}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){drop}<LSEP>[](symbol){x1}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){x2}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){drop}<LSEP>[](symbol){x2}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){x2}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){wassersteinpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){var}<LSEP>[](symbol){x1}<LEND>[argument 2; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){x2}<LEND>[argument 3; call](){}<LSEP>[](symbol){var}<LSEP>[](symbol){x2}<LEND>[](symbol){check}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){wassersteinpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LSEP>[](symbol){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){var}<LSEP>[](symbol){x1}<LEND>[argument 2; call](){}<LSEP>[](symbol){colMeans}<LSEP>[](symbol){x2}<LEND>[argument 3; call](){}<LSEP>[](symbol){var}<LSEP>[](symbol){x2}<LEND>[](symbol){check}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){indexFTP}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){folder}<LSEP>[](symbol){base}<LSEP>[](symbol){is.file.if.has.dot}<LSEP>[](symbol){exclude.latest.bin}<LSEP>[](symbol){fast}<LSEP>[](symbol){sleep}<LSEP>[](symbol){dir}<LSEP>[](symbol){filename}<LSEP>[](symbol){overwrite}<LSEP>[](symbol){quiet}<LSEP>[](symbol){progbar}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){checkSuggestedPackage}<LSEP>[argument 0; litteral](str){RCurl}<LSEP>[argument 1; litteral](str){rdwd::indexFTP}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){^https}<LSEP>[](symbol){base}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){base should start with ftp://,...}<LSEP>[](symbol){base}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){folder}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){currentfindex}<LSEP>[argument 1; litteral](str){currentgindex}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){base}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){dwdbase}<LSEP>[](symbol){gridbase}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Reading current index tree fil...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){fast}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){readLines}<LSEP>[argument 0; litteral](str){ftp://opendata.dwd.de/weather/...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){checkSuggestedPackage}<LSEP>[argument 0; litteral](str){data.table}<LSEP>[argument 1; litteral](str){rdwd::indexFTP with fast=TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){data.table}<LSEP>[](symbol){fread}<LEND>[argument 0; litteral](str){ftp://opendata.dwd.de/weather/...}<LSEP>[argument 1; litteral](str){\n}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[](symbol){V1}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Processing index tree file...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){urlpart}<LSEP>[litteral](str){"https://opendata.dwd.de/clim...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){folder}<LSEP>[argument 1; litteral](str){currentgindex}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){urlpart}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){observations_germany/climate}<LSEP>[argument 1; litteral](str){grids_germany}<LSEP>[](symbol){urlpart}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){grep}<LSEP>[](symbol){urlpart}<LSEP>[](symbol){tree}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){href=}<LEND>[argument 1; litteral](str){[}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[](symbol){urlpart}<LSEP>[argument 1; litteral](str){/}<LSEP>[](symbol){tree}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){/"}<LEND>[argument 1; litteral](str){[}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){tree}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){tree}<LEND>[argument 1; call](){}<LSEP>[](symbol){dirname}<LSEP>[](symbol){tree}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){folder}<LSEP>[](symbol){tree}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){quiet}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Determining the content of the }<LEND>[argument 1; 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litteral](str){INDEX_of_DWD_}<LEND>[argument 1; call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){/}<LSEP>[argument 1; litteral](str){_}<LSEP>[](symbol){filename}<LEND>[argument 2; litteral](str){.txt}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){outfile}<LEND>[call](){}<LSEP>[](symbol){newFilename}<LSEP>[](symbol){outfile}<LSEP>[](symbol){overwrite}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LSEP>[](symbol){quiet}<LEND>[statement 20; call](){}<LSEP>[](symbol){write.table}<LSEP>[](symbol){finalpaths}<LSEP>[](symbol){outfile}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 21; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){finalpaths}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.read.csv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){filename}<LSEP>[](symbol){transpose}<LSEP>[](symbol){ind.metafile}<LSEP>[](symbol){loc.metafile}<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; 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){is.null}<LSEP>[](symbol){loc.metafile}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Locus metafile not pr...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ind.metafile}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Individual metafile n...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){df0}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LSEP>[](symbol){filename}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 8; control flow](){if}<LSEP>[](symbol){transpose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){df0}<LEND>[call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){df0}<LEND>[statement 9; 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call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){loc.metrics}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){gl.recalc.metrics}<LSEP>[](symbol){gl}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){gl.recalc.metrics}<LSEP>[](symbol){gl}<LEND>[statement 33; 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){ Added or updated }<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[argument 2; litteral](str){to the other$ind.metrics slot.\n}<LEND>[statement 34; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ind.metafile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ind.metrics}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LSEP>[](symbol){ind.metafile}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){id}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){ind.metrics}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: mandatory id colu...}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){gl}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ind.metrics}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[](symbol){id}<LEND>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: id in the individ...}<LSEP>[argument 1; litteral](str){id in the input data file, or ...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<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>[argument 0; litteral](str){pop}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){ind.metrics}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: pop column absent f...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[](symbol){ind.metrics}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[](symbol){id}<LEND>[](symbol){individuals}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[](symbol){pop}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](str){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){gl}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[](symbol){pop}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[](symbol){ind.metrics}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[](symbol){id}<LEND>[](symbol){individuals}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[](symbol){pop}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ind.metrics}<LSEP>[](symbol){pop}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[](symbol){pop}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Added }<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[argument 2; litteral](str){ to the other$ind.metrics slot.\n}<LEND>[statement 35; assign](){<-}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){gl.compliance.check}<LSEP>[](symbol){gl}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 36; 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 37; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){gl}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){parse_ticket_create_body}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){body}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){match_result}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stringr}<LSEP>[](symbol){str_match}<LEND>[](symbol){body}<LSEP>[argument 1; litteral](str){Ticket (\\d+) created\\.}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){match_result}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[](symbol){body}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 2; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){match_result}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){rt_ticket_create}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){queue}<LSEP>[](symbol){requestor}<LSEP>[](symbol){subject}<LSEP>[](symbol){cc}<LSEP>[](symbol){admin_cc}<LSEP>[](symbol){owner}<LSEP>[](symbol){status}<LSEP>[](symbol){priority}<LSEP>[](symbol){initial_priority}<LSEP>[](symbol){final_priority}<LSEP>[](symbol){time_estimated}<LSEP>[](symbol){starts}<LSEP>[](symbol){due}<LSEP>[](symbol){text}<LSEP>[](symbol){custom_field}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){params}<LEND>[call](){}<LSEP>[](symbol){compact}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](str){ticket/new}<LSEP>[](symbol){queue}<LSEP>[](symbol){requestor}<LSEP>[](symbol){subject}<LSEP>[](symbol){cc}<LSEP>[](symbol){admin_cc}<LSEP>[](symbol){owner}<LSEP>[](symbol){status}<LSEP>[](symbol){priority}<LSEP>[](symbol){initial_priority}<LSEP>[](symbol){final_priority}<LSEP>[](symbol){time_estimated}<LSEP>[](symbol){starts}<LSEP>[](symbol){due}<LSEP>[](symbol){text}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ticket_content}<LEND>[call](){}<LSEP>[](symbol){construct_newline_pairs}<LSEP>[](symbol){params}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){exists}<LSEP>[argument 0; litteral](str){custom_field}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){custom_field}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cf}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){\nCF-%s: %s}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){custom_field}<LEND>[](symbol){custom_field}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ticket_content}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){ticket_content}<LSEP>[](symbol){cf}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){url}<LEND>[call](){}<LSEP>[](symbol){rt_url}<LSEP>[argument 0; litteral](str){ticket}<LSEP>[argument 1; litteral](str){new}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){response}<LEND>[call](){}<LSEP>[](symbol){rt_POST}<LSEP>[](symbol){url}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){ticket_content}<LEND>[](symbol){...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){parsed}<LEND>[call](){}<LSEP>[](symbol){parse_ticket_create_body}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[statement 6; call](){}<LSEP>[](symbol){stopforstatus}<LSEP>[](symbol){response}<LEND>[statement 7; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[statement 8; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){parsed}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl2demerelate}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){gl}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){x}<LSEP>[](symbol){gl}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: genlight object...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Detected Presence...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){gl}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){gl}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x1}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[litteral](real){2.000000}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x1}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){ }<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x1}<LEND>[argument 1; litteral](str){_1}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x2}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[litteral](real){2.000000}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x2}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[litteral](real){2.000000}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x2}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){ }<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x2}<LEND>[argument 1; litteral](str){_2}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){-}<LSEP>[argument 1; litteral](str){_}<LEND>[argument 2; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 3; litteral](logical){TRUE}<LEND>[statement 21; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){/}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 3; litteral](logical){TRUE}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){|}<LSEP>[argument 1; litteral](str){_}<LEND>[argument 2; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 3; litteral](logical){TRUE}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){cbind.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){gl}<LEND>[](symbol){x}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 24; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 25; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){df}<LEND>[argument 1; litteral](real){1.000000}<LEND>[litteral](str){Sample-ID}<LEND>[statement 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){df}<LEND>[argument 1; litteral](real){2.000000}<LEND>[litteral](str){Population}<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){df}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl2faststructure}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){outfile}<LSEP>[](symbol){outpath}<LSEP>[](symbol){probar}<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; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Fatal Error: genlight object...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Detected Presence...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){nc}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 10; control flow](){if}<LSEP>[](symbol){probar}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){pb}<LEND>[call](){}<LSEP>[](symbol){txtProgressBar}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](logical){NA}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){zz}<LEND>[call](){}<LSEP>[](symbol){file}<LSEP>[](symbol){outfilespec}<LSEP>[argument 1; litteral](str){w}<LEND>[statement 12; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dummy}<LEND>[call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colSums}<LSEP>[](symbol){dummy}<LSEP>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dummy}<LSEP>[](symbol){}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dummy}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){dummy}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){9.000000}<LEND>[](symbol){dummy}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){dummy}<LEND>[call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dummy}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){dummy}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dummy}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LSEP>[](symbol){dummy}<LEND>[statement 6; call](){}<LSEP>[](symbol){write}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){dummy}<LEND>[](symbol){outfilespec}<LSEP>[argument 2; litteral](str){\t}<LSEP>[](symbol){nc}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){probar}<LEND>[true branch; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){pb}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[statement 13; call](){}<LSEP>[](symbol){close}<LSEP>[](symbol){zz}<LEND>[statement 14; control flow](){if}<LSEP>[](symbol){probar}<LEND>[true branch; call](){}<LSEP>[](symbol){close}<LSEP>[](symbol){pb}<LEND>[statement 15; 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){paste0}<LSEP>[argument 0; litteral](str){Saved faststructure file: }<LSEP>[](symbol){outfilespec}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 16; 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}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Consists of}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){individuals and }<LEND>[argument 3; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 4; litteral](str){loci.}<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>[argument 0; litteral](NULL){NULL}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){globalCostMatrix}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){lm}<LSEP>[](symbol){step.matrix}<LSEP>[](symbol){window.function}<LSEP>[](symbol){native}<LSEP>[](symbol){seed}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.stepPattern}<LSEP>[](symbol){step.matrix}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){step.matrix is no stepMatrix o...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){lm}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){lm}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){nsteps}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){step.matrix}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){seed}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cm}<LSEP>[](symbol){seed}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cm}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){n}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cm}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lm}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){sm}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){n}<LSEP>[](symbol){m}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){native}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wm}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){FALSE}<LSEP>[](symbol){n}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){wm}<LEND>[argument 1; call](){}<LSEP>[](symbol){window.function}<LEND>[argument 0; call](){}<LSEP>[](symbol){row}<LSEP>[](symbol){wm}<LEND>[argument 1; call](){}<LSEP>[](symbol){col}<LSEP>[](symbol){wm}<LEND>[](symbol){n}<LSEP>[](symbol){m}<LSEP>[](symbol){...}<LEND>[litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){storage.mode}<LSEP>[](symbol){wm}<LEND>[litteral](str){logical}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){storage.mode}<LSEP>[](symbol){lm}<LEND>[litteral](str){double}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){storage.mode}<LSEP>[](symbol){cm}<LEND>[litteral](str){double}<LEND>[statement 5; 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litteral](real){1.000000}<LSEP>[](symbol){nsteps}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dir}<LSEP>[](symbol){s}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ii}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dir}<LSEP>[](symbol){s}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){jj}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dir}<LSEP>[](symbol){s}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){ii}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){jj}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cc}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dir}<LSEP>[](symbol){s}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){cc}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clist}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cm}<LSEP>[](symbol){ii}<LSEP>[](symbol){jj}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clist}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clist}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){cc}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lm}<LSEP>[](symbol){ii}<LSEP>[](symbol){jj}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){minc}<LEND>[call](){}<LSEP>[](symbol){which.min}<LSEP>[](symbol){clist}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){minc}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cm}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){clist}<LSEP>[](symbol){minc}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sm}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[](symbol){minc}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){cm}<LSEP>[](symbol){sm}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){out}<LSEP>[](symbol){stepPattern}<LEND>[](symbol){step.matrix}<LEND>[statement 8; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){mtgorder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LSEP>[](symbol){display}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.foldermtg}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){mtgorder applies to an object ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){classes}<LSEP>[argument 1; litteral](str){all}<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){classes}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LEND>[](symbol){SCALE}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; litteral](str){SYMBOL}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'classes' argument does not ma...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){all}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){classes}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LEND>[](symbol){SCALE}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; litteral](str){SYMBOL}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){topo}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){topology}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){mat.order}<LEND>[call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){topo}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){topo}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){nchar}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){v.order}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){mat.order}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){which}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){cl}<LSEP>[](symbol){classes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){cl}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.order}<LEND>[argument 1; call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){cl}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){display}<LEND>[true branch; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){utils.dist.binary}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<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; 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; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Binary distance measures are...}<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){method}<LEND>[call](){}<LSEP>[](symbol){tolower}<LSEP>[](symbol){method}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){method}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){simple}<LSEP>[argument 1; litteral](str){jaccard}<LSEP>[argument 2; litteral](str){dice}<LSEP>[argument 3; litteral](str){sorenson}<LSEP>[argument 4; litteral](str){czekanowski}<LSEP>[argument 5; litteral](str){phi}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){version}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){as.folderh.foldermtg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wrongclasses}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){classes}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LEND>[](symbol){SYMBOL}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){wrongclasses}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Element(s) of 'classes' which ...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LSEP>[](symbol){wrongclasses}<LEND>[argument 1; litteral](str){', '}<LEND>[argument 2; litteral](str){'}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){scales}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){classes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){classe}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LEND>[](symbol){SYMBOL}<LEND>[](symbol){classe}<LEND>[argument 2; litteral](str){SCALE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){order.scale}<LEND>[call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){scales}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){scales}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){scales}<LSEP>[](symbol){order.scale}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){classes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LSEP>[](symbol){order.scale}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){isduplic}<LEND>[call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){scales}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){isduplic}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The classes given by 'classes'...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){tab}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tab}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tab}<LEND>[](symbol){tab}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){tab}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){listdf}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){tab}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){listdf}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 13; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){classes}<LEND>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){classe}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){scal}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){scales}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vertices}<LEND>[call](){}<LSEP>[](symbol){rownames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tab}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){scal}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){tab}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){character}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){tab}<LEND>[argument 1; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tab}<LEND>[](symbol){tab}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){tab}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){classe}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){scal}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){vertex}<LSEP>[](symbol){vertices}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){comp}<LEND>[call](){}<LSEP>[](symbol){mtgcomponents}<LSEP>[](symbol){x}<LSEP>[](symbol){vertex}<LSEP>[](symbol){scal}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){comp}<LEND>[call](){}<LSEP>[](symbol){intersect}<LSEP>[](symbol){comp}<LEND>[argument 1; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){tab}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tab}<LSEP>[](symbol){comp}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){vertex}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){listdf}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){scal}<LEND>[](symbol){tab}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){listdf}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){listdf}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 15; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){listdf}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){listdf}<LSEP>[](symbol){k}<LEND>[](symbol){}<LSEP>[argument 2; 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litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){listdf}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 3; litteral](logical){TRUE}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){classes}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){classes}<LEND>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){keyk}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dfk}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){listdf}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){foldh}<LEND>[call](){}<LSEP>[](symbol){appendtofolderh}<LSEP>[](symbol){foldh}<LSEP>[](symbol){dfk}<LSEP>[](symbol){keyk}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){foldh}<LEND>[](symbol){classes}<LEND>[statement 19; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){foldh}<LSEP>[argument 1; litteral](str){keys}<LEND>[litteral](NULL){NULL}<LEND>[statement 20; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){foldh}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){summary.ata}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){evaluation}<LSEP>[argument 1; litteral](str){final_ids}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The ata object input is missin...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){Below}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){Above}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){Within}<LEND>[call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){success}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){Below}<LSEP>[](symbol){Within}<LSEP>[](symbol){Above}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){Constraint}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){evaluation}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){success}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){Constraint}<LSEP>[](symbol){success}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){aggregated}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ATA was formed by}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){final_ids}<LEND>[argument 2; litteral](str){items from}<LEND>[argument 3; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){final_setids}<LEND>[argument 4; litteral](str){sets.}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ATA was formed by}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){final_ids}<LEND>[argument 2; litteral](str){items.}<LEND>[statement 8; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){\nMethod:}<LEND>[argument 1; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){method}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){\n\n}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){success}<LSEP>[](symbol){Within}<LEND>[argument 2; litteral](str){ / }<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){evaluation}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 4; litteral](str){ constraints within the define...}<LSEP>[argument 5; litteral](str){}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){method}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){wdm}<LEND>[argument 1; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){refined}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){final_ids}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){initial_ids}<LEND>[argument 1; litteral](str){item(s) replaced after refinem...}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){method}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){permutated}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Final item selection was refin...}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){aggregated}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Data were aggregated by user-d...}<LEND>[statement 13; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nATA form was created in}<LEND>[argument 1; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){runtime}<LEND>[argument 2; call](){}<LSEP>[](symbol){units}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){runtime}<LEND>[argument 3; litteral](str){\n}<LEND>[statement 14; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){success}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){print.discdd.predict}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){dist.print}<LSEP>[](symbol){prox.print}<LSEP>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){misclassed}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){alloc}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){confusion.mat}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rsums}<LEND>[call](){}<LSEP>[](symbol){rowSums}<LSEP>[](symbol){alloc}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){csums}<LEND>[call](){}<LSEP>[](symbol){colSums}<LSEP>[](symbol){alloc}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){wellclass}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){alloc}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){namesalloc}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){alloc}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){alloc}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){alloc}<LSEP>[](symbol){rsums}<LEND>[argument 2; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){wellclass}<LSEP>[](symbol){rsums}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){alloc}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){alloc}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){csums}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){csums}<LEND>[argument 2; litteral](logical){NA}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){alloc}<LEND>[](symbol){namesalloc}<LEND>[statement 8; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){misallocation ratio (computed ...}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){misclassed}<LEND>[argument 1; litteral](str){\n\n}<LEND>[statement 10; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 11; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){alloc}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){...}<LEND>[statement 12; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){prediction}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){dist.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){distances between groups and c...}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){distances}<LEND>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){prox.print}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){------------------------------...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){groups-classes proximity index\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){proximities}<LEND>[](symbol){...}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matipl2d}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){method}<LSEP>[](symbol){varwL}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){matipl2d now applies to an obj...}<LEND>[statement 1; 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 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){is.numeric}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Non numeric column(s) in the d...}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 4; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){gaussiand}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){varwL}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){l2d}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){method}<LSEP>[argument 3; litteral](NULL){NULL}<LSEP>[argument 4; litteral](NULL){NULL}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){l2d}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){method}<LSEP>[argument 3; litteral](NULL){NULL}<LSEP>[argument 4; litteral](NULL){NULL}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){l2d}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){j}<LEND>[](symbol){method}<LSEP>[argument 3; litteral](NULL){NULL}<LSEP>[argument 4; litteral](NULL){NULL}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){l2d}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){method}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varwL}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varwL}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){l2d}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){method}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varwL}<LSEP>[](symbol){i}<LEND>[argument 4; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varwL}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){l2d}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){j}<LEND>[](symbol){method}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varwL}<LSEP>[](symbol){i}<LEND>[argument 4; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varwL}<LSEP>[](symbol){j}<LEND>[](symbol){W}
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call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; 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assign](){<-}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){links}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){from}<LSEP>[argument 1; litteral](str){to}<LSEP>[argument 2; litteral](str){weight}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodes}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){ind.names}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){nodes}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){name}<LSEP>[argument 1; litteral](str){pop}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nodes}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){m}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){nodes}<LEND>[litteral](str){name}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){network}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){igraph}<LSEP>[](symbol){graph_from_data_frame}<LEND>[](symbol){links}<LSEP>[](symbol){nodes}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){colors}<LEND>[call](){}<LSEP>[](symbol){rainbow}<LEND>[argument 0; call](){}<LSEP>[](symbol){nlevels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){my_colors}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){colors}<LEND>[argument 1; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){my_colors}<LSEP>[litteral](str){red}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stats}<LSEP>[](symbol){quantile}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){links}<LSEP>[](symbol){weight}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){alpha}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){network.FS}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){igraph}<LSEP>[](symbol){delete_edges}<LEND>[](symbol){network}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){igraph}<LSEP>[](symbol){E}<LEND>[](symbol){network}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){links}<LSEP>[](symbol){weight}<LEND>[](symbol){q}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){fr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){layout.name}<LSEP>[litteral](str){Fruchterman-Reingold layout}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){igraph}<LSEP>[](symbol){layout_with_fr}<LEND>[](symbol){network.FS}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){kk}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){layout.name}<LSEP>[litteral](str){Kamada-Kawai layout}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){igraph}<LSEP>[](symbol){layout_with_kk}<LEND>[](symbol){network.FS}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){drl}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){layout.name}<LSEP>[litteral](str){DrL Graph layout}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){igraph}<LSEP>[](symbol){layout_with_drl}<LEND>[](symbol){network.FS}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){title}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){title}<LSEP>[argument 1; litteral](str){\n[}<LSEP>[](symbol){layout.name}<LSEP>[argument 3; litteral](str){]}<LEND>[statement 25; control flow](){if}<LSEP>[](symbol){node.label}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){node.label}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){igraph}<LSEP>[](symbol){V}<LEND>[](symbol){network}<LEND>[](symbol){name}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){node.label}<LSEP>[litteral](logical){NA}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){node.label.size}<LSEP>[litteral](logical){NA}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){node.label.color}<LSEP>[litteral](logical){NA}<LEND>[statement 26; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){network.FS}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){links}<LSEP>[](symbol){weight}<LEND>[](symbol){node.size}<LSEP>[](symbol){my_colors}<LSEP>[argument 6; litteral](str){#555555}<LSEP>[](symbol){node.label}<LSEP>[](symbol){node.label.color}<LSEP>[](symbol){node.label.size}<LSEP>[](symbol){l}<LSEP>[](symbol){title}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){legend}<LSEP>[argument 0; litteral](str){bottomleft}<LEND>[argument 1; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[](symbol){colors}<LSEP>[argument 3; litteral](str){n}<LSEP>[argument 4; litteral](real){20.000000}<LSEP>[argument 5; litteral](real){3.000000}<LSEP>[argument 6; litteral](real){1.000000}<LSEP>[](symbol){colors}<LSEP>[argument 8; litteral](logical){FALSE}<LEND>[argument 9; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.100000}<LSEP>[argument 1; litteral](real){0.100000}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 29; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){as.data.frame.folderh}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){row.names}<LSEP>[](symbol){optional}<LSEP>[](symbol){...}<LSEP>[](symbol){elt}<LSEP>[](symbol){key}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){keys}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){keys}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){keys}<LSEP>[](symbol){key}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[](symbol){elt}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){k}<LSEP>[](symbol){j}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){If}<LSEP>[](symbol){elt}<LSEP>[argument 2; litteral](str){ is the}<LSEP>[](symbol){j}<LSEP>[argument 4; litteral](str){-th element of the folderh, th...}<LSEP>[](symbol){j}<LSEP>[argument 6; litteral](str){-th element of attr(x, 'keys')...}<LSEP>[argument 7; litteral](str){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){datf}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){j}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){cnames}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){datf}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[statement 1; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){datf}<LEND>[call](){}<LSEP>[](symbol){merge}<LSEP>[](symbol){datf}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){keys}<LSEP>[](symbol){i}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cnames}<LEND>[call](){}<LSEP>[](symbol){union}<LEND>[argument 0; call](){}<LSEP>[](symbol){union}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){keys}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){keys}<LSEP>[](symbol){i}<LEND>[](symbol){cnames}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){datf}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){datf}<LSEP>[](symbol){cnames}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){datf}<LEND>[call](){}<LSEP>[](symbol){merge}<LSEP>[](symbol){datf}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){k}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){keys}<LSEP>[](symbol){k}<LEND>[argument 3; litteral](logical){FALSE}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){datf}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){as.folder.folderh}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){elt}<LSEP>[](symbol){key}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){dfx}<LEND>[call](){}<LSEP>[](symbol){as.data.frame.folderh}<LSEP>[](symbol){x}<LSEP>[](symbol){elt}<LSEP>[](symbol){key}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){fold}<LEND>[call](){}<LSEP>[](symbol){as.folder.data.frame}<LSEP>[](symbol){dfx}<LSEP>[](symbol){key}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){fold}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){fpcad}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){xf}<LSEP>[](symbol){group.name}<LSEP>[](symbol){gaussiand}<LSEP>[](symbol){windowh}<LSEP>[](symbol){normed}<LSEP>[](symbol){centered}<LSEP>[](symbol){data.centered}<LSEP>[](symbol){data.scaled}<LSEP>[](symbol){common.variance}<LSEP>[](symbol){nb.factors}<LSEP>[](symbol){nb.values}<LSEP>[](symbol){sub.title}<LSEP>[](symbol){plot.eigen}<LSEP>[](symbol){plot.score}<LSEP>[](symbol){nscore}<LSEP>[](symbol){filename}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){xf}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){xf}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){fpcad applies to a data frame ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){xf}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){xf}<LSEP>[](symbol){group.name}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){xf}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){group.name}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){xf}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){xf has no column named '}<LSEP>[](symbol){group.name}<LSEP>[argument 2; litteral](str){'.}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xf}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){xf}<LEND>[](symbol){group.name}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){group.name}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xf}<LSEP>[](symbol){}<LSEP>[](symbol){group.name}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){as.folder}<LSEP>[](symbol){xf}<LSEP>[](symbol){group.name}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){last.column.name}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[litteral](str){group}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){group}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){nb.groups}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LSEP>[](symbol){group}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){levgroup}<LEND>[call](){}<LSEP>[](symbol){levels}<LSEP>[](symbol){group}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.refcryptoexchangesurl}<LSEP>[litteral](str){https://api.twelvedata.com/cry...}<LEND>[assign](){<-}<LSEP>[](symbol){ref_crypto_exchanges}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){as}<LSEP>[](symbol){apikey}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){apikey}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){apikey}<LEND>[call](){}<LSEP>[](symbol){.get_apikey}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){as}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){as}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){.refcryptoexchangesurl}<LSEP>[argument 1; litteral](str){?}<LSEP>[argument 2; litteral](str){&apikey=}<LSEP>[](symbol){apikey}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){accessed}<LEND>[call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[argument 1; litteral](str){UTC}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RcppSimdJson}<LSEP>[](symbol){fload}<LEND>[](symbol){qry}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){as}<LSEP>[argument 1; litteral](str){raw}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){res}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){res}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){status}<LEND>[argument 1; litteral](str){ok}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){message}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){data}<LEND>[](symbol){dat}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[argument 0; litteral](str){rbind}<LSEP>[](symbol){dat}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){dat}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The API returned NULL data.}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dat}<LSEP>[argument 1; litteral](str){accessed}<LEND>[](symbol){accessed}<LEND>[](symbol){dat}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.aggregate_data}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){data}<LSEP>[](symbol){link_maximum}<LSEP>[](symbol){conti}<LSEP>[](symbol){flow}<LSEP>[](symbol){origin}<LSEP>[](symbol){destination}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){link_maximum}<LSEP>[](symbol){origin}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){link_maximum}<LSEP>[](symbol){destination}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){conti}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){flow}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){conti}<LEND>[argument 3; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){origin}<LSEP>[](symbol){destination}<LEND>[statement 1; call](){}<LSEP>[](symbol){setnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){origin}<LSEP>[argument 1; litteral](str){destination}<LSEP>[argument 2; litteral](str){V1}<LSEP>[argument 3; litteral](str){V2}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){origin}<LSEP>[argument 1; litteral](str){destination}<LSEP>[argument 2; litteral](str){flow}<LSEP>[argument 3; litteral](str){conti}<LEND>[statement 2; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){conti}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){conti}<LEND>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){flow}<LEND>[argument 3; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){origin}<LSEP>[](symbol){destination}<LEND>[statement 1; call](){}<LSEP>[](symbol){setnames}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){origin}<LSEP>[argument 1; litteral](str){destination}<LSEP>[argument 2; litteral](str){V1}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){origin}<LSEP>[argument 1; litteral](str){destination}<LSEP>[argument 2; litteral](str){flow}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){.link_rate}<LSEP>[](symbol){data}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){data}<LEND>[assign](){<-}<LSEP>[](symbol){.link_max}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){data}<LSEP>[](symbol){size_center}<LSEP>[](symbol){conti}<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; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){list_center}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; 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call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){destination}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){origin}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){sdestinationck_origin}<LEND>[](symbol){size_center}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){conti}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){origin}<LEND>[](symbol){list_center}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){list_center}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){destination}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){origin}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){sdestinationck_origin}<LEND>[](symbol){size_center}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){destination}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){origin}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){sdestinationck_origin}<LEND>[](symbol){size_center}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<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){$}<LSEP>[](symbol){data}<LSEP>[](symbol){origin}<LEND>[](symbol){list_center}<LEND>[](symbol){}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){which.max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){link}<LEND>[](symbol){}<LEND>[assign](){<-}<LSEP>[](symbol){.link_rate}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){data}<LSEP>[](symbol){flow}<LSEP>[](symbol){origin}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sdestinationck_origin}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){flow}<LEND>[argument 3; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){origin}<LEND>[statement 1; call](){}<LSEP>[](symbol){setnames}<LSEP>[](symbol){sdestinationck_origin}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){origin}<LSEP>[argument 1; litteral](str){V1}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){origin}<LSEP>[argument 1; litteral](str){sdestinationck_origin}<LEND>[statement 2; call](){}<LSEP>[](symbol){setkey}<LSEP>[](symbol){sdestinationck_origin}<LSEP>[argument 1; litteral](str){origin}<LEND>[statement 3; call](){}<LSEP>[](symbol){setkey}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](str){origin}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){merge}<LSEP>[](symbol){data}<LSEP>[](symbol){sdestinationck_origin}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){link}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){flow}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){data}<LSEP>[](symbol){sdestinationck_origin}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){data}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){try_tibble}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){df}<LSEP>[](symbol){coerce}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){coerce}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){df}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){suppressMessages}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){requireNamespace}<LSEP>[argument 0; litteral](str){tibble}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){df}<LEND>[statement 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tibble}<LSEP>[](symbol){as_tibble}<LEND>[](symbol){df}<LEND>[assign](){<-}<LSEP>[](symbol){tidy_long_search_result}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){result}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){result}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){result}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){No matching results.}<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 1; assign](){<-}<LSEP>[](symbol){dfs}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){result}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rdf}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){r}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){rdf}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){[ \\.]*}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){rdf}<LEND>[](symbol){rdf}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){all_dfs}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[](symbol){rbind.data.frame}<LSEP>[](symbol){dfs}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){all_dfs}<LSEP>[](symbol){id}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){ticket/}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){all_dfs}<LSEP>[](symbol){id}<LEND>[statement 4; call](){}<LSEP>[](symbol){try_tibble}<LSEP>[](symbol){all_dfs}<LEND>[assign](){<-}<LSEP>[](symbol){rt_ticket_search}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){query}<LSEP>[](symbol){orderby}<LSEP>[](symbol){format}<LSEP>[](symbol){fields}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){format}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){l}<LSEP>[argument 1; litteral](str){s}<LSEP>[argument 2; litteral](str){i}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](logical){FALSE}<LSEP>[argument 1; litteral](str){Invalid choice of format, '}<LSEP>[](symbol){format}<LSEP>[argument 3; litteral](str){'. 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.collapse.recursive}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){tloc}<LSEP>[](symbol){tpop}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){tpop}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LSEP>[](symbol){tpop}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){tpop}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){tpop}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: Parameter tpop ...}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){typically small (e.g. 3)\n}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){tloc}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){tloc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: Parameter tloc ...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LSEP>[](symbol){verbose}<LEND>[statement 11; 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){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: Parameter verbo...}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Recursively amalgamating pop...}<LSEP>[](symbol){tpop}<LSEP>[argument 2; litteral](str){or fewer fixed differences\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating initial fixed di...}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){fd}<LEND>[call](){}<LSEP>[](symbol){gl.fixed.diff}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[](symbol){tloc}<LSEP>[argument 3; litteral](real){0.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){fd.hold}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd}<LSEP>[](symbol){fd}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 15; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){tpop}<LEND>[body; 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){\nSetting tpop to}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){count}<LSEP>[litteral](real){0.000000}<LEND>[statement 2; control flow](){repeat}<LSEP>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){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){Iteration:}<LSEP>[](symbol){count}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){fdcoll}<LEND>[call](){}<LSEP>[](symbol){gl.collapse}<LSEP>[](symbol){fd}<LSEP>[](symbol){i}<LSEP>[](symbol){tloc}<LSEP>[](symbol){verbose}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: All populations amalg...}<LSEP>[](symbol){count}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 1; control flow](){break}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fdcoll}<LSEP>[](symbol){fd}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){fd.hold}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){\n No further amalgamation of...}<LSEP>[](symbol){count}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 1; control flow](){break}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){fd.hold}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fdcoll}<LSEP>[](symbol){fd}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){fd}<LSEP>[](symbol){fdcoll}<LEND>[statement 16; 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; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){tloc}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Using absolute fixed diffe...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Using fixed differences de...}<LSEP>[](symbol){tloc}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Number of fixed difference...}<LSEP>[](symbol){tpop}<LSEP>[argument 2; litteral](str){(}<LEND>[argument 3; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){tpop}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){4.000000}<LEND>[argument 4; litteral](str){%)\n}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){fd}<LSEP>[](symbol){fdcoll}<LEND>[statement 18; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fdcoll}<LSEP>[](symbol){gl}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd}<LSEP>[](symbol){gl}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd}<LSEP>[](symbol){fd}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd}<LSEP>[](symbol){pcfd}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd}<LSEP>[](symbol){nobs}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd}<LSEP>[](symbol){nloc}<LEND>[argument 5; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd}<LSEP>[](symbol){expfpos}<LEND>[argument 6; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd}<LSEP>[](symbol){sdfpos}<LEND>[argument 7; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fd}<LSEP>[](symbol){pval}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){l}<LEND>[litteral](str){fd}<LEND>[statement 21; 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){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 -- if ...}<LSEP>[argument 7; litteral](str){ [[6]] $sdfpos -- if t...}<LSEP>[argument 8; litteral](str){ [[7]] $prob -- if tes...}<LEND>[statement 22; 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){\nCompleted:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 23; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){l}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){getrow.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){name}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){object}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){getrow.folder applies to an ob...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){objk}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){object}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xf}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){objk}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){objk}<LEND>[](symbol){name}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){object}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){xf}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){utils.read.dart}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){filename}<LSEP>[](symbol){nas}<LSEP>[](symbol){topskip}<LSEP>[](symbol){lastmetric}<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; 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){is.null}<LSEP>[](symbol){topskip}<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){ Topskip not provided. }<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tdummy}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LSEP>[](symbol){filename}<LSEP>[](symbol){nas}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[argument 3; litteral](real){20.000000}<LSEP>[argument 4; litteral](logical){FALSE}<LSEP>[argument 5; litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nskip}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tdummy}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){*}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nskip}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){topskip}<LSEP>[](symbol){nskip}<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){Setting topskip to}<LSEP>[](symbol){nskip}<LSEP>[argument 2; litteral](str){.\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Could not determine the number...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Reading in the SNP data\n}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){snpraw}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LSEP>[](symbol){filename}<LSEP>[](symbol){nas}<LSEP>[](symbol){topskip}<LSEP>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](logical){TRUE}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){lastmetric}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lmet}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){lastmetric}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){snpraw}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lmet}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Could not determine number of ...}<LSEP>[](symbol){lastmetric}<LSEP>[argument 2; litteral](str){!\n}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lmet}<LSEP>[](symbol){lastmetric}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){ind.names}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){snpraw}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){lmet}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){snpraw}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){ind.names}<LEND>[call](){}<LSEP>[](symbol){trimws}<LSEP>[](symbol){ind.names}<LSEP>[argument 1; litteral](str){both}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ind.names}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){ind.names}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Individual names are ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ind.names}<LEND>[call](){}<LSEP>[](symbol){make.unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){ind.names}<LEND>[argument 1; litteral](str){_}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){datas}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){snpraw}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){lmet}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){snpraw}<LEND>[statement 13; assign](){=}<LSEP>[](symbol){nrows}<LSEP>[litteral](NULL){NULL}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){nrows}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){gnrows}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){datas}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gnrows}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gnrows}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nrows}<LSEP>[](symbol){gnrows}<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){ Detected}<LSEP>[](symbol){nrows}<LSEP>[argument 2; litteral](str){row format.\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The DArT format must be either...}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){stdmetricscols}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){lmet}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Added the following locus metr...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){snpraw}<LEND>[](symbol){stdmetricscols}<LEND>[argument 1; litteral](str){ }<LEND>[argument 1; litteral](str){.\n}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){covmetrics}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){snpraw}<LSEP>[](symbol){}<LSEP>[](symbol){stdmetricscols}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){covmetrics}<LSEP>[](symbol){clone}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){\\|.*}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){covmetrics}<LSEP>[](symbol){AlleleID}<LEND>[](symbol){T}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){spp}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){.+-+(\\d{1,3}):.+}<LSEP>[argument 1; litteral](str){\\1}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){covmetrics}<LSEP>[](symbol){AlleleID}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){covmetrics}<LSEP>[](symbol){uid}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){covmetrics}<LSEP>[](symbol){clone}<LEND>[](symbol){spp}<LSEP>[argument 2; litteral](str){-}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){tt}<LEND>[call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){covmetrics}<LSEP>[](symbol){uid}<LEND>[statement 22; 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){Number of rows per clone (shou...}<LSEP>[](symbol){nrows}<LSEP>[argument 2; litteral](str){s):}<LEND>[argument 3; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tt}<LEND>[argument 4; litteral](str){\n }<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){nrows}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tt}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: The no. rows per Cl...}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){nind}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){datas}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){nsnp}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){covmetrics}<LEND>[](symbol){nrows}<LEND>[statement 26; 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){Recognised:}<LSEP>[](symbol){nind}<LSEP>[argument 2; litteral](str){individuals and}<LSEP>[](symbol){nsnp}<LSEP>[argument 4; litteral](str){ SNPs in a}<LSEP>[](symbol){nrows}<LSEP>[argument 6; litteral](str){row format using}<LSEP>[](symbol){filename}<LSEP>[argument 8; litteral](str){\n}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){nrows}<LSEP>[](symbol){nind}<LSEP>[](symbol){nsnp}<LSEP>[](symbol){covmetrics}<LSEP>[](symbol){datas}<LEND>[statement 28; 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}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 29; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){out}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){hellingerpar}<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; assign](){<-}<LSEP>[](symbol){affin}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){sqrt}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){var1}<LSEP>[](symbol){var2}<LEND>[argument 1; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){localtestdir}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){packdir}<LSEP>[](symbol){folder}<LSEP>[](symbol){file}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){packagePath}<LEND>[](symbol){packdir}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){/}<LSEP>[](symbol){folder}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){file}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){/}<LSEP>[](symbol){file}<LEND>[](symbol){out}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){importRRD}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){filename}<LSEP>[](symbol){cf}<LSEP>[](symbol){start}<LSEP>[](symbol){end}<LSEP>[](symbol){step}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){cf}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){start}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){end}<LEND>[argument 3; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){step}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){.Deprecated}<LSEP>[](symbol){read_rra}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){.Deprecated}<LSEP>[](symbol){read_rrd}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){as.foldert.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){method}<LSEP>[](symbol){ind}<LSEP>[](symbol){timecol}<LSEP>[](symbol){nvar}<LSEP>[](symbol){same.rows}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){ind}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){ind}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[](symbol){ind}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){timecol}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){timecol}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[](symbol){timecol}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){method}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){method}<LSEP>[](symbol){method}<LEND>[statement 4; call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){method}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){name.x}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){name.g}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){timecol}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){name.x}<LSEP>[argument 1; litteral](str){is not a data frame.}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){timecol}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){name.g}<LSEP>[argument 1; litteral](str){ is not a column name of }<LSEP>[](symbol){name.x}<LSEP>[argument 3; litteral](str){.}<LSEP>[argument 4; litteral](str){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){jind}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[](symbol){ind}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){jg}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[](symbol){timecol}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){jg}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){g}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.ordered}<LSEP>[](symbol){g}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){Date}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){g}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){POSIXlt}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){g}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){POSIXct}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){g}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){name.x}<LSEP>[argument 1; litteral](str){[, }<LSEP>[](symbol){name.g}<LSEP>[argument 3; litteral](str){]}<LSEP>[argument 4; litteral](str){ must be of class 'numeric', '...}<LSEP>[argument 5; litteral](str){}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){as.ordered}<LSEP>[](symbol){g}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){glev}<LEND>[call](){}<LSEP>[](symbol){levels}<LSEP>[](symbol){g}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){fold}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 11; control flow](){for}<LSEP>[](symbol){l}<LSEP>[](symbol){glev}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fold.l}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){g}<LSEP>[](symbol){l}<LEND>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){fold.l}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fold.l}<LSEP>[](symbol){}<LSEP>[](symbol){jind}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){fold}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){fold}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fold.l}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){jind}<LSEP>[](symbol){jg}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fold}<LEND>[](symbol){glev}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){foldt}<LEND>[call](){}<LSEP>[](symbol){foldert}<LSEP>[](symbol){fold}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){jg}<LEND>[argument 2; litteral](str){union}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[argument 0; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){same.rows}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[argument 0; litteral](str){union}<LSEP>[](symbol){same.rows}<LEND>[argument 2; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){same.rows}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){same.rows}<LSEP>[litteral](logical){TRUE}<LEND>[statement 1; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){When method==2, the returned '...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){jind}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[](symbol){ind}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){jt}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[](symbol){timecol}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){jt}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Duplicated column names: Sever...}<LSEP>[](symbol){timecol}<LSEP>[argument 2; litteral](str){\nThe first of these column is...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){jt}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){jt}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){cnames}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){jt}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nvar}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){fold}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){i}<LSEP>[litteral](real){0.000000}<LEND>[statement 7; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){jt}<LSEP>[](symbol){nvar}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xj}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){jt}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nvar}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){xj}<LEND>[](symbol){cnames}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){xj}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){jind}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){fold}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){fold}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){xj}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){jt}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){jt}<LSEP>[](symbol){nvar}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){fold}<LSEP>[](symbol){ncol}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[](symbol){jt}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){The number of columns expected...}<LSEP>[argument 1; litteral](str){The last columns of x data fra...}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){times}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){t}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){fold}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){foldt}<LEND>[call](){}<LSEP>[](symbol){foldert}<LSEP>[](symbol){fold}<LEND>[argument 1; call](){}<LSEP>[](symbol){ordered}<LSEP>[](symbol){times}<LSEP>[](symbol){times}<LEND>[argument 2; litteral](str){union}<LSEP>[argument 3; litteral](str){union}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){foldt}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){hardTh}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LSEP>[](symbol){thld}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){y}<LEND>[](symbol){thld}<LEND>[](symbol){y}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rt_ticket_properties}<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){show}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){response}<LEND>[call](){}<LSEP>[](symbol){rt_GET}<LSEP>[](symbol){url}<LSEP>[](symbol){...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){Ticket \\d+ does not exist\\.}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[statement 3; call](){}<LSEP>[](symbol){stopforstatus}<LSEP>[](symbol){response}<LEND>[statement 4; call](){}<LSEP>[](symbol){parse_rt_properties}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matddjensen}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.folder}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){x must be an object of class '...}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[body; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){ddjensen}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){j}<LEND>[statement 4; call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){distances}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){WC_FST_Diploids_2Alleles}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){Sample_Mat}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){sample_sizes}<LEND>[call](){}<LSEP>[](symbol){rowSums}<LSEP>[](symbol){Sample_Mat}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){n_ave}<LEND>[call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){sample_sizes}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){n_pops}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){Sample_Mat}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){r}<LSEP>[](symbol){n_pops}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){n_c}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_pops}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){sample_sizes}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_pops}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_pops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){p_freqs}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sample_Mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sample_Mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[](symbol){sample_sizes}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){p_ave}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LSEP>[](symbol){p_freqs}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_pops}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){s2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p_freqs}<LSEP>[](symbol){p_ave}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_pops}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n_ave}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){s2}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){h_freqs}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sample_Mat}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){sample_sizes}<LEND>[statement 10; assign](){=}<LSEP>[](symbol){h_ave}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){sample_sizes}<LSEP>[](symbol){h_freqs}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_pops}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){dtw}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){dist.method}<LSEP>[](symbol){step.pattern}<LSEP>[](symbol){window.type}<LSEP>[](symbol){keep.internals}<LSEP>[](symbol){distance.only}<LSEP>[](symbol){open.end}<LSEP>[](symbol){open.begin}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lm}<LSEP>[litteral](NULL){NULL}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){y}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){dist.method}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Argument dist.method does not ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){x}<LEND>[true branch; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){utils.hamming}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){str1}<LSEP>[](symbol){str2}<LSEP>[](symbol){r}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){strmin}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){str1}<LEND>[argument 1; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){str2}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){str1}<LEND>[call](){}<LSEP>[](symbol){substr}<LSEP>[](symbol){str1}<LSEP>[](symbol){r}<LSEP>[](symbol){strmin}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){str2}<LEND>[call](){}<LSEP>[](symbol){substr}<LSEP>[](symbol){str2}<LSEP>[](symbol){r}<LSEP>[](symbol){strmin}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){str1}<LSEP>[argument 1; litteral](str){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){str2}<LSEP>[argument 1; litteral](str){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){uniqs}<LEND>[call](){}<LSEP>[](symbol){union}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){H}<LEND>[call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){uniqs}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){uniqs}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){uniq}<LEND>[range; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){uniqs}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){H}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){H}<LEND>[argument 1; call](){}<LSEP>[](symbol){%*%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x}<LSEP>[](symbol){uniq}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){y}<LSEP>[](symbol){uniq}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[](symbol){H}<LEND>[](symbol){strmin}<LEND>[statement 9; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){result}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.utils.fdsim}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){gl}<LSEP>[](symbol){poppair}<LSEP>[](symbol){obs}<LSEP>[](symbol){sympatric}<LSEP>[](symbol){reps}<LSEP>[](symbol){delta}<LSEP>[](symbol){verbose}<LEND>[body; 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){Starting gl.utils.fdsim: Using...}<LEND>[statement 1; 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){class}<LSEP>[](symbol){gl}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: Input data must b...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){poppair}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){gl}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: Population A misl...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){poppair}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){gl}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: Population B misl...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){poppair}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pair}<LEND>[call](){}<LSEP>[](symbol){gl.keep.pop}<LSEP>[](symbol){gl}<LSEP>[](symbol){poppair}<LSEP>[argument 2; litteral](logical){FALSE}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: Must specify two ...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Comparing }<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){poppair}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){and}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){poppair}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 4; litteral](str){\n}<LEND>[statement 6; 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>[argument 1; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){pair}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){pair}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of observed fixed differ...}<LSEP>[](symbol){obs}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){rf}<LEND>[call](){}<LSEP>[](symbol){gl.percent.freq}<LSEP>[](symbol){pair}<LSEP>[](symbol){verbose}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){rfA}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rf}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rf}<LSEP>[](symbol){popn}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){poppair}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 9; 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Please be patient\n}<LEND>[statement 18; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){reps}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){pair}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rfA}<LSEP>[](symbol){frequency}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rfB}<LSEP>[](symbol){frequency}<LEND>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; 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call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbinom}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){szA}<LSEP>[](symbol){pbA}<LEND>[](symbol){szA}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){simB}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbinom}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){szB}<LSEP>[](symbol){pbB}<LEND>[](symbol){szB}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fd}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){simA}<LSEP>[](symbol){i}<LEND>[](symbol){szA}<LEND>[argument 1; 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call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){falsepos}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Estimated SD of the count of f...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){falsepos}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Prob that observed count of}<LSEP>[](symbol){obs}<LSEP>[argument 2; litteral](str){are false positives:}<LSEP>[](symbol){nprob}<LSEP>[argument 4; litteral](str){\n}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){obs}<LSEP>[](symbol){mn}<LSEP>[](symbol){sdev}<LSEP>[](symbol){nprob}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed gl.utils.fdsim\n\n}<LEND>[statement 25; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){l}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){summary.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){summ.fold}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){object}<LSEP>[](symbol){summary}<LSEP>[](symbol){...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){summ.fold}<LSEP>[argument 1; litteral](str){same.rows}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){same.rows}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){summ.fold}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.filter.taglength}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){lower}<LSEP>[](symbol){upper}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence ...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){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; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Data must include...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){upper}<LSEP>[](symbol){lower}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'upper' m...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tmp}<LSEP>[](symbol){upper}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){upper}<LSEP>[](symbol){lower}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){lower}<LSEP>[](symbol){tmp}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){lower}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){lower}<LSEP>[argument 1; litteral](real){250.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lower}<LSEP>[litteral](real){20.000000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){upper}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){upper}<LSEP>[argument 1; litteral](real){250.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'upper' m...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){upper}<LSEP>[litteral](real){69.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){n0}<LEND>[call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Initial no. of loci =}<LSEP>[](symbol){n0}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){tags}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){TrimmedSequence}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){nchar.tags}<LEND>[call](){}<LSEP>[](symbol){nchar}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){tags}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Removing loci with taglength <}<LSEP>[](symbol){lower}<LSEP>[argument 2; litteral](str){and >}<LSEP>[](symbol){upper}<LSEP>[argument 4; litteral](str){\n}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){nchar.tags}<LSEP>[](symbol){lower}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){nchar.tags}<LSEP>[](symbol){upper}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){index}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<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 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of loci deleted =}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n0}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x2}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 20; 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){Summary of filtered dataset\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Sequence Tag Length >=}<LSEP>[](symbol){lower}<LSEP>[argument 2; litteral](str){and Sequence Tag Length <=}<LSEP>[](symbol){upper}<LSEP>[argument 4; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x2}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of individuals:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x2}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of populations: }<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x2}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x2}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x2}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 24; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x2}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.merge.pop}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){old}<LSEP>[](symbol){new}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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; 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){>=}<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){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){old}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Renaming a population\n}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){old}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Merging a list of populations ...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: At least one old ...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){new}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: A new population ...}<LEND>[statement 7; 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 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){old}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Renaming}<LSEP>[](symbol){old}<LSEP>[argument 2; litteral](str){as}<LSEP>[](symbol){new}<LSEP>[argument 4; litteral](str){\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Merging}<LSEP>[](symbol){old}<LSEP>[argument 2; litteral](str){into}<LSEP>[](symbol){new}<LSEP>[argument 4; litteral](str){\n}<LEND>[statement 9; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){old}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){old}<LSEP>[](symbol){i}<LEND>[](symbol){new}<LEND>[statement 10; 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 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){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 12; 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 13; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){mvdst}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){variant}<LSEP>[](symbol){inverted}<LEND>[body; call](){}<LSEP>[](symbol){mvdtt}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){dst}<LSEP>[](symbol){variant}<LSEP>[](symbol){inverted}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){ada.default}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){test.x}<LSEP>[](symbol){test.y}<LSEP>[](symbol){loss}<LSEP>[](symbol){type}<LSEP>[](symbol){iter}<LSEP>[](symbol){nu}<LSEP>[](symbol){bag.frac}<LSEP>[](symbol){model.coef}<LSEP>[](symbol){bag.shift}<LSEP>[](symbol){max.iter}<LSEP>[](symbol){delta}<LSEP>[](symbol){verbose}<LSEP>[](symbol){...}<LSEP>[](symbol){na.action}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){match.call}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cl}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){ada}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){type}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){type}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){type}<LSEP>[litteral](str){discrete}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){loss}<LEND>[true branch; assign](){=}<LSEP>[](symbol){loss}<LSEP>[litteral](str){exponential}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){loss}<LEND>[call](){}<LSEP>[](symbol){tolower}<LSEP>[](symbol){loss}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){loss}<LSEP>[argument 1; litteral](str){e}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){loss}<LSEP>[argument 1; litteral](str){ada}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){loss}<LSEP>[litteral](str){exponential}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){loss}<LSEP>[argument 1; litteral](str){l}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){loss}<LSEP>[argument 1; litteral](str){l2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){loss}<LSEP>[litteral](str){logistic}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){This procedure requires a resp...}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){lev}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.factor}<LSEP>[](symbol){y}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lev}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Currently this procedure can n...}<LEND>[statement 11; assign](){=}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LEND>[statement 12; assign](){=}<LSEP>[](symbol){test.dat}<LSEP>[litteral](logical){FALSE}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){test.y}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){tlev}<LSEP>[litteral](NULL){NULL}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){test.x}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){tlev}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.factor}<LSEP>[](symbol){test.y}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){test.x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){test.x}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){test.dat}<LSEP>[litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tlev}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){test.x must be the testing dat...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){test.x}<LSEP>[litteral](NULL){NULL}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lev}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rt_ticket_attachment_content}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){ticket_id}<LSEP>[](symbol){attachment_id}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){url}<LEND>[call](){}<LSEP>[](symbol){rt_url}<LSEP>[argument 0; litteral](str){ticket}<LSEP>[](symbol){ticket_id}<LSEP>[argument 2; litteral](str){attachments}<LSEP>[](symbol){attachment_id}<LSEP>[argument 4; litteral](str){content}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){response}<LEND>[call](){}<LSEP>[](symbol){rt_GET}<LSEP>[](symbol){url}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){...}<LEND>[statement 2; call](){}<LSEP>[](symbol){stopforstatus}<LSEP>[](symbol){response}<LEND>[](symbol){response}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.report.heterozygosity}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){method}<LSEP>[](symbol){n.invariant}<LSEP>[](symbol){plot}<LSEP>[](symbol){boxplot}<LSEP>[](symbol){range}<LSEP>[](symbol){cex.labels}<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){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){plot}<LSEP>[litteral](logical){FALSE}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; 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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){Reporting Heterozygosity by In...}<LEND>[statement 1; 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 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){No. of individuals =}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Miniumum Observed Heterozygo...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Maximum Observed Heterozygos...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 5; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Average Observed Heterozygos...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 2; litteral](str){\n\n}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Results returned as a datafr...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No outliers detected\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Outliers detected -- \n}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){outliers}<LEND>[statement 14; 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){par}<LSEP>[](symbol){op}<LEND>[statement 15; 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 16; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){df}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){utils.recalc.avgpic}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){hold}<LSEP>[](symbol){x}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Fatal Error: genlight object...}<LEND>[statement 1; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){updateIndexes}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dwdlocal}<LSEP>[](symbol){grdlocal}<LSEP>[](symbol){metaforce}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){rdwd$}<LEND>[argument 1; call](){}<LSEP>[](symbol){getwd}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){getwd must be in package root ...}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){begintime}<LEND>[call](){}<LSEP>[](symbol){Sys.time}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){messaget}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){...}<LEND>[body; call](){}<LSEP>[](symbol){message}<LEND>[argument 0; call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[argument 1; litteral](str){%T - }<LEND>[](symbol){...}<LEND>[statement 3; control flow](){if}<LSEP>[](symbol){dwdlocal}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){dwdfiles}<LEND>[call](){}<LSEP>[](symbol){readLines}<LSEP>[argument 0; litteral](str){DWDdata/INDEX_of_DWD_.txt}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){Indexing FTP Server at dwdbase...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dwdfiles}<LEND>[call](){}<LSEP>[](symbol){indexFTP}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 4; control flow](){if}<LSEP>[](symbol){grdlocal}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){grdfiles}<LEND>[call](){}<LSEP>[](symbol){readLines}<LSEP>[argument 0; litteral](str){DWDdata/INDEX_of_DWD_grids.txt}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){Indexing FTP Server at gridbas...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){grdfiles}<LEND>[call](){}<LSEP>[](symbol){indexFTP}<LSEP>[argument 0; litteral](str){currentgindex}<LSEP>[argument 1; litteral](str){grids}<LSEP>[](symbol){gridbase}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 5; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){Calling createIndex...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){createIndex}<LSEP>[](symbol){dwdfiles}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){metaforce}<LSEP>[argument 3; litteral](logical){TRUE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 7; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){Saving index rda files into pa...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){fileIndex}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){index}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){metaIndex}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){index}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){geoIndex}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){index}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){gridIndex}<LSEP>[](symbol){grdfiles}<LEND>[statement 12; call](){}<LSEP>[](symbol){save}<LSEP>[](symbol){fileIndex}<LSEP>[argument 1; litteral](str){data/fileIndex.rda}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 13; call](){}<LSEP>[](symbol){save}<LSEP>[](symbol){metaIndex}<LSEP>[argument 1; litteral](str){data/metaIndex.rda}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 14; call](){}<LSEP>[](symbol){save}<LSEP>[](symbol){geoIndex}<LSEP>[argument 1; litteral](str){data/geoIndex.rda}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 15; call](){}<LSEP>[](symbol){save}<LSEP>[](symbol){gridIndex}<LSEP>[argument 1; litteral](str){data/gridIndex.rda}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 16; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; 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call](){}<LSEP>[](symbol){checkSuggestedPackage}<LSEP>[argument 0; litteral](str){XML}<LSEP>[argument 1; litteral](str){updateIndexes}<LEND>[statement 34; assign](){<-}<LSEP>[](symbol){format_url}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){dwdbase}<LSEP>[argument 1; litteral](str){/subdaily/standard_format/form...}<LEND>[statement 35; assign](){<-}<LSEP>[](symbol){format_html}<LEND>[call](){}<LSEP>[](symbol){readLines}<LSEP>[](symbol){format_url}<LSEP>[argument 1; litteral](str){UTF-8}<LEND>[statement 36; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Saving and compressing formatI...}<LEND>[statement 37; assign](){<-}<LSEP>[](symbol){format_html}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){&nbsp;}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){format_html}<LEND>[statement 38; assign](){<-}<LSEP>[](symbol){format_html}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){&#176;}<LSEP>[argument 1; litteral](str){degree}<LSEP>[](symbol){format_html}<LEND>[statement 39; 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assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rv_df}<LSEP>[](symbol){Quelle}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){substr}<LSEP>[](symbol){urls}<LSEP>[argument 1; litteral](real){76.000000}<LSEP>[argument 2; litteral](real){1000.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){rv}<LSEP>[](symbol){nrow}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){rv_df}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){sortDF}<LEND>[](symbol){rv_df}<LSEP>[argument 1; litteral](str){Par}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){rv_df}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){berryFunctions}<LSEP>[](symbol){sortDF}<LEND>[](symbol){rv_df}<LSEP>[argument 1; litteral](str){Kurz}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 5; assign](){<-}<LSEP>[variable; 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call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){dt}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){ }<LEND>[argument 3; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dt}<LSEP>[argument 1; litteral](str){units}<LEND>[argument 4; litteral](str){.}<LEND>[statement 61; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){index}<LSEP>[](symbol){checks}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.map.interactive}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){matrix}<LSEP>[](symbol){standard}<LSEP>[](symbol){symmetric}<LSEP>[](symbol){ind.circles}<LSEP>[](symbol){pop.labels}<LSEP>[](symbol){pop.labels.cex}<LSEP>[](symbol){provider}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pkg}<LSEP>[litteral](str){leaflet}<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){pkg}<LSEP>[litteral](str){leaflet.minicharts}<LEND>[statement 3; 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; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){genlight}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Not a valid genlight object pr...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlong}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No valid coordinates are suppl...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlong}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){lat}<LSEP>[argument 1; litteral](str){lon}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Coordinates under gl@other$lat...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){matrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){matrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The dimension of the provided ...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){cols}<LEND>[call](){}<LSEP>[](symbol){rainbow}<LEND>[argument 0; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){cols}<LEND>[call](){}<LSEP>[](symbol){substr}<LSEP>[](symbol){cols}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){7.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; 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call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){to}<LSEP>[argument 1; litteral](str){lon}<LEND>[argument 2; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){from}<LSEP>[argument 1; litteral](str){lat}<LEND>[argument 3; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){to}<LSEP>[argument 1; litteral](str){lat}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matrix}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[](symbol){lcols}<LSEP>[argument 6; litteral](real){10.000000}<LSEP>[argument 7; litteral](real){1.000000}<LEND>[argument 8; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){matrix}<LSEP>[](symbol){T}<LEND>[argument 9; litteral](real){0.800000}<LEND>[statement 12; call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){leaflet}<LSEP>[](symbol){addProviderTiles}<LEND>[](symbol){provider}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){mtgrank}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LSEP>[](symbol){parent.class}<LSEP>[](symbol){sibling.classes}<LSEP>[](symbol){relative}<LSEP>[](symbol){from}<LSEP>[](symbol){rank.name}<LSEP>[](symbol){display}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.foldermtg}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){mtgrank applies to an object o...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){from}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){from}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){from}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){origin}<LSEP>[argument 1; litteral](str){end}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){from must be 'origin' or 'end'.}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){classes}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){scal}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){classes}<LSEP>[](symbol){SYMBOL}<LEND>[](symbol){classe}<LEND>[argument 2; litteral](str){SCALE}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){parent.class}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){parent.class}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){classes}<LSEP>[](symbol){SCALE}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){scal}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){SYMBOL}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){parent.class}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){parent.class argument cannot b...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){sibling.classes}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){classes}<LSEP>[](symbol){SYMBOL}<LEND>[](symbol){sibling.classes}<LEND>[argument 2; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){cut.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){breaks}<LSEP>[](symbol){labels}<LSEP>[](symbol){include.lowest}<LSEP>[](symbol){right}<LSEP>[](symbol){dig.lab}<LSEP>[](symbol){ordered_result}<LSEP>[](symbol){cutcol}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){colnum}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){x}<LSEP>[](symbol){is.numeric}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){cutcol}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){fileType}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){file}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](str){fileTypeError}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){file}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){.zip$}<LSEP>[](symbol){file}<LEND>[litteral](str){data}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){.txt$}<LSEP>[](symbol){file}<LEND>[litteral](str){meta}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){Standort.txt$}<LSEP>[](symbol){file}<LEND>[litteral](str){multia}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){standard_format}<LSEP>[](symbol){file}<LEND>[litteral](str){stand}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){.gz$}<LSEP>[](symbol){file}<LEND>[litteral](str){radar}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){.tar.gz$}<LSEP>[](symbol){file}<LEND>[litteral](str){binary}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){.asc.gz$}<LSEP>[](symbol){file}<LEND>[litteral](str){raster}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){.nc.gz$}<LSEP>[](symbol){file}<LEND>[litteral](str){nc}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){.tar$}<LSEP>[](symbol){file}<LEND>[litteral](str){asc}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){.grib2.bz2$}<LSEP>[](symbol){file}<LEND>[litteral](str){grib2}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){fileTypeError}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){fileType failed for the follow...}<LEND>[argument 1; call](){}<LSEP>[](symbol){truncMessage}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){file}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){out}<LSEP>[argument 1; litteral](str){fileTypeError}<LEND>[argument 1; litteral](str){: }<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){out}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.grm}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){plotheatmap}<LSEP>[](symbol){verbose}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pkg}<LSEP>[litteral](str){rrBLUP}<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){pkg}<LSEP>[litteral](str){gplots}<LEND>[statement 3; 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 4; 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 5; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 6; 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 7; 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 8; 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 9; 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 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Detected Tag Presence/Absenc...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Population assignments not d...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](str){pop1}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){gg_color_hue}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){hues}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){15.000000}<LSEP>[argument 1; litteral](real){375.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){hcl}<LSEP>[](symbol){hues}<LSEP>[argument 1; litteral](real){65.000000}<LSEP>[argument 2; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){colors_pop_temp}<LEND>[call](){}<LSEP>[](symbol){gg_color_hue}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){colors_pop_temp}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){pop}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){cols_pops}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){colors_pop_temp}<LEND>[](symbol){colors_pop_temp}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){cols_pops}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){pop}<LSEP>[argument 1; litteral](str){colour}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){df_pops}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){pop}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){df_pops}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){pop}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){cols_pops}<LEND>[call](){}<LSEP>[](symbol){merge}<LSEP>[](symbol){df_pops}<LSEP>[](symbol){cols_pops}<LSEP>[argument 2; litteral](str){pop}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){G}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){rrBLUP}<LSEP>[](symbol){A.mat}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){...}<LEND>[statement 21; assign](){=}<LSEP>[](symbol){cool}<LEND>[call](){}<LSEP>[](symbol){rainbow}<LSEP>[argument 0; litteral](real){50.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rgb2hsv}<LEND>[argument 0; call](){}<LSEP>[](symbol){col2rgb}<LSEP>[argument 0; litteral](str){cyan}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rgb2hsv}<LEND>[argument 0; call](){}<LSEP>[](symbol){col2rgb}<LSEP>[argument 0; litteral](str){blue}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 22; assign](){=}<LSEP>[](symbol){warm}<LEND>[call](){}<LSEP>[](symbol){rainbow}<LSEP>[argument 0; litteral](real){50.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rgb2hsv}<LEND>[argument 0; call](){}<LSEP>[](symbol){col2rgb}<LSEP>[argument 0; litteral](str){red}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rgb2hsv}<LEND>[argument 0; call](){}<LSEP>[](symbol){col2rgb}<LSEP>[argument 0; litteral](str){yellow}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 23; assign](){=}<LSEP>[](symbol){cols}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){cool}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){warm}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){mypalette}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){colorRampPalette}<LSEP>[](symbol){cols}<LEND>[argument 0; litteral](real){255.000000}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){plotheatmap}<LSEP>[](symbol){T}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){gplots}<LSEP>[](symbol){heatmap.2}<LEND>[](symbol){G}<LSEP>[](symbol){mypalette}<LSEP>[argument 2; litteral](str){column}<LEND>[argument 3; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){cols_pops}<LSEP>[](symbol){colour}<LEND>[argument 4; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){cols_pops}<LSEP>[](symbol){colour}<LEND>[argument 5; litteral](str){none}<LSEP>[argument 6; litteral](str){none}<LSEP>[argument 7; litteral](str){none}<LSEP>[argument 8; litteral](str){Probability of identity by des...}<LEND>[statement 1; call](){}<LSEP>[](symbol){legend}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.800000}<LEND>[argument 2; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){cols_pops}<LSEP>[](symbol){pop}<LEND>[argument 3; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){cols_pops}<LSEP>[](symbol){colour}<LEND>[argument 4; litteral](real){0.750000}<LSEP>[argument 5; litteral](str){Populations}<LEND>[statement 26; 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 27; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){G}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.genleastcost}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){fric.raster}<LSEP>[](symbol){gen.distance}<LSEP>[](symbol){NN}<LSEP>[](symbol){pathtype}<LSEP>[](symbol){plotpath}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pkg}<LSEP>[litteral](str){gdistance}<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){pkg}<LSEP>[litteral](str){mmod}<LEND>[statement 3; 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 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){NN}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){pathtype}<LSEP>[argument 1; litteral](str){leastcost}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){NN is not specified!\nPlease s...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dist.type}<LSEP>[litteral](logical){NA}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){D}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){Gst.Hedrick}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){Gst.Nei}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){dist.type}<LSEP>[litteral](str){pop}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){Kosman}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){Smouse}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){propShared}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){dist.type}<LSEP>[litteral](str){ind}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){dist.type}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No valid genetic distance type...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){xy}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){No projected coordinates in @o...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){xy}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlong}<LEND>[](symbol){}<LEND>[argument 2; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matddchisqsympar}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){freq}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){diag}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){freq}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){freq}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){freq}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){freq}<LEND>[body; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){ddchisqsympar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){freq}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){freq}<LSEP>[](symbol){j}<LEND>[statement 3; call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){distances}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){warn_user_edit_warnings}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){body}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){parts}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stringr}<LSEP>[](symbol){str_split}<LEND>[](symbol){body}<LSEP>[argument 1; litteral](str){\n# User \\d+ updated\\.}<LEND>[statement 1; 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){length}<LSEP>[](symbol){parts}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parts}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stringr}<LSEP>[](symbol){str_detect}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parts}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){: }<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){parts}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){rt_user_edit}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){user_id}<LSEP>[](symbol){password}<LSEP>[](symbol){name}<LSEP>[](symbol){email_address}<LSEP>[](symbol){real_name}<LSEP>[](symbol){organization}<LSEP>[](symbol){privileged}<LSEP>[](symbol){disabled}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){params}<LEND>[call](){}<LSEP>[](symbol){compact}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){name}<LSEP>[](symbol){password}<LSEP>[](symbol){email_address}<LSEP>[](symbol){real_name}<LSEP>[](symbol){organization}<LSEP>[](symbol){privileged}<LSEP>[](symbol){disabled}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){user_info}<LEND>[call](){}<LSEP>[](symbol){construct_newline_pairs}<LSEP>[](symbol){params}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){url}<LEND>[call](){}<LSEP>[](symbol){rt_url}<LSEP>[argument 0; litteral](str){user}<LSEP>[](symbol){user_id}<LSEP>[argument 2; litteral](str){edit}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){response}<LEND>[call](){}<LSEP>[](symbol){rt_POST}<LSEP>[](symbol){url}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){user_info}<LEND>[](symbol){...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stringr}<LSEP>[](symbol){str_detect}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[argument 1; litteral](str){User \\d+ updated\\.}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warn_user_edit_warnings}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 5; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Failed to edit user }<LSEP>[](symbol){user_id}<LSEP>[argument 2; litteral](str){.\n\n}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){getcol.foldert}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){name}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.foldert}<LSEP>[](symbol){object}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){getcol.foldert applies to an o...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](str){[}<LSEP>[](symbol){name}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){xf}<LEND>[call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){object}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){xf}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){remove_all_na_cols}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){df}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){Filter}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){x}<LEND>[](symbol){df}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){ata_glpk}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){time_limit}<LSEP>[](symbol){message}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ata}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Not an 'ata' object}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){opts}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lp}<LEND>[call](){}<LSEP>[](symbol){initProbGLPK}<LEND>[statement 3; call](){}<LSEP>[](symbol){addRowsGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mat}<LEND>[statement 4; call](){}<LSEP>[](symbol){addColsGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mat}<LEND>[statement 5; call](){}<LSEP>[](symbol){setObjDirGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){max}<LEND>[](symbol){GLP_MAX}<LSEP>[](symbol){GLP_MIN}<LEND>[statement 6; call](){}<LSEP>[](symbol){setObjCoefsGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){n_lpvar}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){obj}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){n_lpvar}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){types}<LEND>[argument 1; litteral](str){B}<LEND>[body; call](){}<LSEP>[](symbol){setColKindGLPK}<LSEP>[](symbol){lp}<LSEP>[](symbol){j}<LSEP>[](symbol){GLP_BV}<LEND>[statement 8; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){n_lpvar}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){types}<LEND>[argument 1; litteral](str){C}<LEND>[body; call](){}<LSEP>[](symbol){setColBndGLPK}<LSEP>[](symbol){lp}<LSEP>[](symbol){j}<LSEP>[](symbol){GLP_LO}<LSEP>[argument 3; litteral](real){0.000000}<LSEP>[argument 4; litteral](real){0.000000}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){negative}<LEND>[true branch; call](){}<LSEP>[](symbol){setColBndGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){n_lpvar}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){GLP_UP}<LSEP>[argument 3; litteral](real){0.000000}<LSEP>[argument 4; litteral](real){0.000000}<LEND>[statement 10; 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){bounds}<LEND>[](symbol){idx}<LEND>[true branch; control flow](){for}<LSEP>[](symbol){j}<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){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bounds}<LEND>[](symbol){idx}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bound}<LEND>[](symbol){lb}<LEND>[](symbol){j}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setColBndGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bounds}<LEND>[](symbol){idx}<LEND>[](symbol){j}<LEND>[](symbol){GLP_UP}<LSEP>[argument 3; litteral](real){0.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bounds}<LEND>[](symbol){ub}<LEND>[](symbol){j}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bound}<LEND>[](symbol){ub}<LEND>[](symbol){j}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setColBndGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bounds}<LEND>[](symbol){idx}<LEND>[](symbol){j}<LEND>[](symbol){GLP_LO}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bounds}<LEND>[](symbol){lb}<LEND>[](symbol){j}<LEND>[argument 4; litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setColBndGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bounds}<LEND>[](symbol){idx}<LEND>[](symbol){j}<LEND>[](symbol){GLP_DB}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bounds}<LEND>[](symbol){lb}<LEND>[](symbol){j}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bounds}<LEND>[](symbol){ub}<LEND>[](symbol){j}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){ind}<LEND>[call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mat}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){ia}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mat}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mat}<LEND>[](symbol){ind}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){ja}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mat}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mat}<LEND>[](symbol){ind}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){ar}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mat}<LEND>[](symbol){ind}<LEND>[statement 15; call](){}<LSEP>[](symbol){loadMatrixGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ar}<LEND>[](symbol){ia}<LSEP>[](symbol){ja}<LSEP>[](symbol){ar}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){dir}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){dir}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){x}<LSEP>[](symbol){GLP_LO}<LSEP>[](symbol){GLP_UP}<LSEP>[](symbol){GLP_FX}<LEND>[statement 17; call](){}<LSEP>[](symbol){setRowsBndsGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mat}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){rhs}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){rhs}<LEND>[](symbol){dir}<LEND>[statement 18; call](){}<LSEP>[](symbol){setMIPParmGLPK}<LSEP>[](symbol){PRESOLVE}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 19; call](){}<LSEP>[](symbol){setMIPParmGLPK}<LSEP>[](symbol){GMI_CUTS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 20; call](){}<LSEP>[](symbol){setMIPParmGLPK}<LSEP>[](symbol){MIR_CUTS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 21; call](){}<LSEP>[](symbol){setMIPParmGLPK}<LSEP>[](symbol){CLQ_CUTS}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 22; call](){}<LSEP>[](symbol){setMIPParmGLPK}<LSEP>[](symbol){MIP_GAP}<LSEP>[argument 1; litteral](real){0.010000}<LEND>[statement 23; call](){}<LSEP>[](symbol){setMIPParmGLPK}<LSEP>[](symbol){TM_LIM}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){1000.000000}<LSEP>[](symbol){time_limit}<LEND>[statement 24; call](){}<LSEP>[](symbol){setMIPParmGLPK}<LSEP>[](symbol){MSG_LEV}<LEND>[argument 1; call](){}<LSEP>[](symbol){ifelse}<LSEP>[](symbol){message}<LSEP>[](symbol){GLP_MSG_ON}<LSEP>[](symbol){GLP_MSG_OFF}<LEND>[statement 25; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){seq_along}<LSEP>[](symbol){opts}<LEND>[body; call](){}<LSEP>[](symbol){setMIPParmGLPK}<LEND>[argument 0; call](){}<LSEP>[](symbol){get}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){opts}<LEND>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){opts}<LSEP>[](symbol){i}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){start_time}<LEND>[call](){}<LSEP>[](symbol){Sys.time}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){code}<LEND>[call](){}<LSEP>[](symbol){solveMIPGLPK}<LSEP>[](symbol){lp}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){solve_time}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[](symbol){start_time}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){status}<LEND>[call](){}<LSEP>[](symbol){switch}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){code}<LEND>[argument 1; litteral](str){optimal solution found}<LSEP>[argument 2; litteral](str){invalid basis}<LSEP>[argument 3; litteral](str){singular matrix}<LSEP>[argument 4; litteral](str){ill-conditioned matrix}<LSEP>[argument 5; litteral](str){invalid bounds}<LSEP>[argument 6; litteral](str){solver failed}<LSEP>[argument 7; litteral](str){objective lower limit reached}<LSEP>[argument 8; litteral](str){objective upper limit reached}<LSEP>[argument 9; litteral](str){iteration limit exceeded}<LSEP>[argument 10; litteral](str){time limit exceeded}<LSEP>[argument 11; litteral](str){no primal feasible solution}<LSEP>[argument 12; litteral](str){no dual feasible solution}<LSEP>[argument 13; litteral](str){root LP optimum not provided}<LSEP>[argument 14; litteral](str){search terminated by application}<LSEP>[argument 15; litteral](str){relative mip gap tolerance rea...}<LSEP>[argument 16; litteral](str){no primal/dual feasible solution}<LSEP>[argument 17; litteral](str){no convergence}<LSEP>[argument 18; litteral](str){numerical instability}<LSEP>[argument 19; litteral](str){invalid data}<LSEP>[argument 20; litteral](str){result out of range}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){optimum}<LEND>[call](){}<LSEP>[](symbol){mipObjValGLPK}<LSEP>[](symbol){lp}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){mipColsValGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){n_lpvar}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){n_forms}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 32; assign](){<-}<LSEP>[](symbol){obj_vars}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){mipColsValGLPK}<LSEP>[](symbol){lp}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){n_lpvar}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 33; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){code}<LSEP>[](symbol){status}<LSEP>[](symbol){optimum}<LSEP>[](symbol){result}<LSEP>[](symbol){obj_vars}<LSEP>[](symbol){start_time}<LSEP>[](symbol){solve_time}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){utils.recalc.freqhomref}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){hold}<LSEP>[](symbol){x}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Fatal Error: genlight object...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Execution terminated\n}<LEND>[statement 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){stop}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SilicoDArT}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){SNP}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Dataset contains mo...}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){ calculations\n}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){FreqHomRef}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){FreqHomRef}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Locus metric FreqHomRef does...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Recalculating locus metric f...}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){FreqHomRef}<LEND>[call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[](symbol){T}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){FreqHomRef}<LEND>[litteral](logical){TRUE}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 15; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.filter.pa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){pop1}<LSEP>[](symbol){pop2}<LSEP>[](symbol){invers}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Private alleles c...}<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}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){pops}<LEND>[call](){}<LSEP>[](symbol){seppop}<LSEP>[](symbol){x}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){p1}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){pops}<LSEP>[](symbol){pop1}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){p2}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){pops}<LSEP>[](symbol){pop2}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){p1alf}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LSEP>[](symbol){p1}<LSEP>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){p2alf}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<LSEP>[](symbol){p2}<LSEP>[](symbol){T}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){priv1}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){p1alf}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){p2alf}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){p1alf}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){p1alf}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){p2alf}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){p1alf}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){priv2}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){p2alf}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){p1alf}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){p2alf}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){p2alf}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){p1alf}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){p2alf}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){pfLoci}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){priv1}<LSEP>[](symbol){priv2}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){x}<LEND>[](symbol){pfLoci}<LEND>[statement 16; control flow](){if}<LSEP>[](symbol){invers}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){index}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){index}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){index}<LSEP>[](symbol){}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 22; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl2gi}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){gl}<LSEP>[](symbol){probar}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; assign](){=}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; assign](){=}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 2; 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}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; 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){Start conversion....\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ptm}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){proc.time}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Please note conversion of bigg...}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Once finished, we recommend to...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){gl}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[statement 5; control flow](){if}<LSEP>[](symbol){probar}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pb}<LEND>[call](){}<LSEP>[](symbol){txtProgressBar}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LSEP>[argument 3; litteral](logical){NA}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){loc.all}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){loc.all}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](str){A/T}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){gl}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){loc.all}<LEND>[argument 1; litteral](real){1.000000}<LEND>[litteral](str){C/G}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){homs1}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){substr}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){loc.all}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){/}<LEND>[argument 2; call](){}<LSEP>[](symbol){substr}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){loc.all}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; litteral](str){}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){hets}<LEND>[call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){loc.all}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){homs2}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){substr}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){loc.all}<LEND>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; litteral](str){/}<LEND>[argument 2; call](){}<LSEP>[](symbol){substr}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){loc.all}<LEND>[argument 1; litteral](real){3.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 3; litteral](str){}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[statement 11; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){ii}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){inp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){inp}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){inp}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xx}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){homs1}<LSEP>[](symbol){ii}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){inp}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xx}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hets}<LSEP>[](symbol){ii}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){inp}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xx}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){homs2}<LSEP>[](symbol){ii}<LEND>[false branch; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xx}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[litteral](str){-/-}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){probar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){setTxtProgressBar}<LSEP>[](symbol){pb}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x}<LEND>[statement 2; 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){\nMatrix converted.. Prepare g...}<LEND>[statement 12; control flow](){if}<LSEP>[](symbol){probar}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){close}<LSEP>[](symbol){pb}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){gen}<LEND>[call](){}<LSEP>[](symbol){df2genind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xx}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[argument 1; litteral](str){/}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){ind.names}<LEND>[argument 4; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){pop}<LEND>[argument 5; litteral](real){2.000000}<LSEP>[argument 6; litteral](str){-}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gen}<LSEP>[](symbol){other}<LEND>[call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){gen}<LEND>[call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){gl}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Finished! Took}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){proc.time}<LEND>[argument 1; litteral](real){3.000000}<LEND>[](symbol){ptm}<LEND>[argument 2; litteral](str){seconds.\n}<LEND>[statement 17; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){gen}
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[](){expression}<LSEP>[litteral](NULL){NULL}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.drop.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; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: genlight object...}<LEND>[statement 7; 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){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence ...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){loc.list}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){first}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){flag}<LSEP>[litteral](str){both}<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){ Both a range of loci and a l...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){loc.list}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){flag}<LSEP>[litteral](str){list}<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){ List of loci to keep has bee...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){first}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){flag}<LSEP>[litteral](str){range}<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){ Range of loci to keep has be...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Fatal Error: Need to specify...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){||}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){flag}<LSEP>[argument 1; litteral](str){both}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){flag}<LSEP>[argument 1; litteral](str){list}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){case}<LSEP>[](symbol){loc.list}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){case}<LEND>[argument 1; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Listed loci}<LSEP>[](symbol){case}<LSEP>[argument 2; litteral](str){not present in the dataset -- ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){loc.list}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loc.list}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){loc.list}<LSEP>[](symbol){case}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){flag}<LSEP>[argument 1; litteral](str){range}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){first}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Lower limit to rang...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){first}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){first}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Upper limit to rang...}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n)}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){last}<LEND>[call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){first}<LSEP>[](symbol){last}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Upper limit is smal...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tmp}<LSEP>[](symbol){first}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){first}<LSEP>[](symbol){last}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){last}<LSEP>[](symbol){tmp}<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){ Deleteing the specified lo...}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){first}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){loc.list}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){list.from.range}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){first}<LSEP>[](symbol){last}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){loc.list}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){loc.list}<LSEP>[](symbol){list.from.range}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){first}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){loc.list}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){first}<LSEP>[](symbol){last}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){loc.list}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: no loci listed to d...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x2}<LSEP>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){loc.names}<LEND>[](symbol){loc.list}<LEND>[statement 1; 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>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){loc.names}<LEND>[](symbol){loc.list}<LEND>[](symbol){}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n Summary of recoded dataset\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Original No. of loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){hold}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of loci deleted:}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){hold}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x2}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of loci retained:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x2}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of individuals:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x2}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 5; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of populations: }<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x2}<LEND>[argument 2; litteral](str){\n\n}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x2}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x2}<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 17; 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 18; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x2}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){ddjensen}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){x1}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){x1}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.vector}<LSEP>[](symbol){x2}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){x2}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x1}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){x1 must be a data frame or a v...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x2}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){x2 must be a data frame or a v...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x1}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x2}<LEND>[](symbol){k}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ncol(x1) != ncol(x2)}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x2}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){x1 and x2 do not have the same...}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x1}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x2}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 9; 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){x1}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lev}<LEND>[call](){}<LSEP>[](symbol){union}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[](symbol){lev}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x2}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[](symbol){lev}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){p1}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x1}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){p2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){x2}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){x2}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){ddjensenpar}<LSEP>[](symbol){p1}<LSEP>[](symbol){p2}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){folderh}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){df1}<LSEP>[](symbol){key1}<LSEP>[](symbol){df2}<LSEP>[](symbol){...}<LSEP>[](symbol){na.rm}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){name.1}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){df1}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){name.2}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){df2}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){name.key}<LEND>[call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){key1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){matchcall}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){name.dots}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matchcall}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){matchcall}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){name.1}<LSEP>[](symbol){name.2}<LSEP>[](symbol){name.key}<LSEP>[](symbol){key1}<LSEP>[argument 4; litteral](str){na.rm}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){dots}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){name.df}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){name.1}<LSEP>[](symbol){name.2}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){X}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){df1}<LSEP>[](symbol){df2}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){X}<LEND>[](symbol){name.df}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){keys}<LSEP>[](symbol){key1}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dots}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){name.X.supp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){name.dots}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dots}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){name.df}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){name.df}<LSEP>[](symbol){name.X.supp}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){X.supp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dots}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dots}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){X}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){X}<LSEP>[](symbol){X.supp}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){X}<LEND>[](symbol){name.df}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){name.keys.supp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){name.dots}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dots}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){name.key}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){name.key}<LSEP>[](symbol){name.keys.supp}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){keys.supp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dots}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dots}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){keys}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){keys}<LEND>[](symbol){keys.supp}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){is.df}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){X}<LSEP>[](symbol){is.data.frame}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){prod}<LSEP>[](symbol){is.df}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Argument(s)}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){name.df}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){is.df}<LEND>[argument 2; litteral](str){is/are no data frame(s).}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){ncolX}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){X}<LSEP>[](symbol){ncol}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){less2col}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){ncolX}<LSEP>[argument 1; litteral](str){<}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){less2col}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The data frame arguments must ...}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){is.atom}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){keys}<LSEP>[](symbol){is.atomic}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){prod}<LSEP>[](symbol){is.atom}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Argument(s)}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){name.keys.supp}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){is.atom}<LEND>[argument 2; litteral](str){is/are no atomic.\n}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){lgkeys}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){keys}<LSEP>[](symbol){length}<LEND>[statement 19; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){lgkeys}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){keys}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){keys}<LSEP>[](symbol){head}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){keys}<LEND>[call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){keys}<LEND>[statement 21; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){keys}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){keyg}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){keys}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dfg1}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){X}<LSEP>[](symbol){k}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dfg2}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){X}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){keyg}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){dfg1}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){There is no}<LSEP>[](symbol){keyg}<LSEP>[argument 2; litteral](str){variable in}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){X}<LEND>[](symbol){k}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){keyg}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){dfg2}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){There is no}<LSEP>[](symbol){keyg}<LSEP>[argument 2; litteral](str){variable in}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){X}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dfg1}<LSEP>[](symbol){}<LSEP>[](symbol){keyg}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){A level of}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){X}<LEND>[](symbol){k}<LEND>[argument 2; litteral](str){[,}<LSEP>[](symbol){keyg}<LSEP>[argument 4; litteral](str){] cannot occur more than once.}<LEND>[statement 6; control flow](){if}<LSEP>[](symbol){na.rm}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){X}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dfg1}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dfg1}<LSEP>[](symbol){}<LSEP>[](symbol){keyg}<LEND>[](symbol){}<LEND>[statement 7; control flow](){if}<LSEP>[](symbol){na.rm}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){X}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dfg2}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dfg2}<LSEP>[](symbol){}<LSEP>[](symbol){keyg}<LEND>[](symbol){}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){keyg}<LSEP>[](symbol){key1}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){foldh}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){X}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){X}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 24; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){foldh}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){name.1}<LSEP>[](symbol){name.2}<LEND>[statement 25; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){foldh}<LEND>[litteral](str){folderh}<LEND>[statement 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){foldh}<LSEP>[argument 1; litteral](str){keys}<LEND>[](symbol){keyg}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){X}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){X}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Xk}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){X}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){foldh}<LEND>[call](){}<LSEP>[](symbol){appendtofolderh}<LSEP>[](symbol){foldh}<LSEP>[](symbol){Xk}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){keys}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 3; litteral](logical){TRUE}<LEND>[statement 28; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){foldh}<LEND>[](symbol){name.df}<LEND>[statement 29; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){foldh}
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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){bin2num}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){dat}<LSEP>[](symbol){len}<LSEP>[](symbol){na}<LSEP>[](symbol){clutter}<LSEP>[](symbol){RX}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){Fna}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){32767}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){Fclutter}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){32766}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){RX}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){na}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){na}<LSEP>[argument 1; litteral](real){32.500000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){clutter}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){clutter}<LSEP>[argument 1; litteral](real){32.500000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){.Fortran}<LSEP>[argument 0; litteral](str){binary_to_num_rx}<LSEP>[](symbol){dat}<LEND>[argument 2; call](){}<LSEP>[](symbol){as.integer}<LSEP>[](symbol){len}<LEND>[argument 3; call](){}<LSEP>[](symbol){as.integer}<LEND>[argument 0; call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){len}<LEND>[](symbol){Fna}<LSEP>[](symbol){Fclutter}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){.Fortran}<LSEP>[argument 0; litteral](str){binary_to_num}<LSEP>[](symbol){dat}<LEND>[argument 2; call](){}<LSEP>[](symbol){as.integer}<LSEP>[](symbol){len}<LEND>[argument 3; call](){}<LSEP>[](symbol){as.integer}<LEND>[argument 0; call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){len}<LEND>[](symbol){Fna}<LSEP>[](symbol){Fclutter}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){out}<LSEP>[](symbol){numeric}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){out}<LSEP>[](symbol){Fna}<LEND>[](symbol){na}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){out}<LSEP>[](symbol){Fclutter}<LEND>[](symbol){clutter}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){out}<LEND>[control flow](){if}<LSEP>[condition; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){bits}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){rawToBits}<LSEP>[](symbol){dat}<LEND>[argument 1; litteral](real){16.000000}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){b2n}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){i}<LEND>[body; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bits}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){val}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; 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call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){12.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){val}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bits}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){14.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){na}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){val}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bits}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){15.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){val}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bits}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){15.000000}<LEND>[argument 1; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.drop.ind}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){ind.list}<LSEP>[](symbol){recalc}<LSEP>[](symbol){mono.rm}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Warning: Parameter 'verbose'...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing Presence/Absence...}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){case}<LSEP>[](symbol){ind.list}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){case}<LEND>[argument 1; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Listed individual}<LSEP>[](symbol){case}<LSEP>[argument 2; litteral](str){not present in the dataset -- ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ind.list}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ind.list}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){ind.list}<LSEP>[](symbol){case}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ind.list}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: no individuals to...}<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){ Deleting individuals}<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){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){ind.names}<LEND>[](symbol){ind.list}<LEND>[statement 11; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 12; control flow](){if}<LSEP>[](symbol){mono.rm}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Deleting monomorphic loc\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.filter.monomorphs}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Resultant dataset m...}<LEND>[statement 14; control flow](){if}<LSEP>[](symbol){recalc}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){gl.recalc.metrics}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Recalculating locus metrics\n}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Locus metrics not recalculat...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){utils.reset.flags}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Summary of recoded dataset\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of individuals:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ No. of populations: }<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){nh}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 19; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}
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