Datasets:

lanesket

/

r-asts-splitted

like 0

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){utils.hwe}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){prob}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argumen

EP>[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>[

>[](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'...}<LE

){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

anch; 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}<L

argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<L

<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ Detected Presence/Absence (S...}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){ applies only to SNP data!\n}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[

d Presence/Absence (S...}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){ applies only to SNP data!\n}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Processing a SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>

SNP dataset\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: Ploidy must be un...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statem

1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Dataset contains mo...}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){ calculations\n}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){hom.ref}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){m}<LEND>[stat

(symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){hom.ref}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){m}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){hom.snp}<LSEP>[](symbol){hom.ref}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){het}<LSEP>[](symbol){hom.ref}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){total}<LSEP>[](symbol){hom.ref}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){p.values}<LSEP>[](symbol){hom.ref}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){boncrit}<LSEP>[](symbol){hom.ref}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){sig}<LSEP>[](symbol){hom.ref}<LEND>[statement 16; assign]

assign](){<-}<LSEP>[](symbol){p.values}<LSEP>[](symbol){hom.ref}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){boncrit}<LSEP>[](symbol){hom.ref}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){sig}<LSEP>[](symbol){hom.ref}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){sig2}<LSEP>[](symbol){hom.ref}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){bonsig}<LSEP>[](symbol){hom.ref}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){bonsig2}<LSEP>[](symbol){hom.ref}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){columns}<LEND>[call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){m}<LEND>[statement 20; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call]()

SEP>[](symbol){columns}<LEND>[call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){m}<LEND>[statement 20; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.ref}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP

<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.snp}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){het}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[]

>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){het}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){utils.prob.hwe}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){het}<LSEP>[](sy

00000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){utils.prob.hwe}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){het}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.ref}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.snp}<LSEP>[](symbol){i}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](sym

<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sig2}<LSEP>[](symbol){i}<LEND>[litteral](logical){NA}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.050000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sig2}<LSEP>[](symbol){i}<LEND>[litteral](str){ns}<LEND>[false branch; control flow](){if

LEND>[argument 1; litteral](real){0.050000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sig2}<LSEP>[](symbol){i}<LEND>[litteral](str){ns}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.050000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.010000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[]

(){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.010000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sig2}<LSEP>[](symbol){i}<LEND>[litteral](str){*}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.010000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; littera

[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.010000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.001000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sig2}<LSEP>[](symbol){i}<LEND>[litteral](str){**}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.001000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[]

){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.001000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sig2}<LSEP>[](symbol){i}<LEND>[litteral](str){***}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){total}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.ref}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){het}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[

](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.ref}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){het}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){hom.snp}<LSEP>[](symbol){i}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){boncrit}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){prob}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){total}<LSEP>[](symbol){i}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LE

bol){[}<LSEP>[](symbol){total}<LSEP>[](symbol){i}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){boncrit}<LSEP>[](symbol){i}<LEND>[

<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p.values}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){boncrit}<LSEP>[](symbol){i}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig2}<LSEP>[](symbol){i}<LEND>[litteral](str){ns}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[

ent 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig2}<LSEP>[](symbol){i}<LEND>[litteral](str){ns}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){bonsig2}<LSEP>[](symbol){i}<LEND>[litteral](str){*}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){hom.ref}<LSEP>[](symbol){het}<LSEP>[](symbol){hom.snp}<LSEP>[](symbo

[litteral](str){*}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){hom.ref}<LSEP>[](symbol){het}<LSEP>[](symbol){hom.snp}<LSEP>[](symbol){total}<LSEP>[](symbol){p.values}<LSEP>[](symbol){sig2}<LSEP>[](symbol){bonsig2}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){columns}<LSEP>[](symbol){result}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Locus}<LSEP>[argument 1; litteral](str){Hom_1}<LSEP>[argument 2; litteral](str){Het}<LSEP>[argument 3; litte

(){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Locus}<LSEP>[argument 1; litteral](str){Hom_1}<LSEP>[argument 2; litteral](str){Het}<LSEP>[argument 3; litteral](str){Hom_2}<LSEP>[argument 4; litteral](str){N}<LSEP>[argument 5; litteral](str){Prob}<LSEP>[argument 6; litteral](str){Sig}<LSEP>[argument 7; litteral](str){BonSig}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){pc}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){sig}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){le

{/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){sig}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){sig}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){pc}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){pc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){pc2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){bonsig}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<L

SEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){bonsig}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){bonsig}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){pc2}<LEND>[call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){pc2}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<L

ition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 29; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){result}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){cramer.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){check}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ is not a data.frame}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](

ol){x}<LEND>[argument 1; litteral](str){ is not a data.frame}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){check}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](s

SEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){x[, }<LSEP>[](symbol){k1}<LSEP>[argument 2; litteral](str){] is converted to a factor}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1

gn](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){assoc}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call]()

ll](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){CramerV}<LSEP>[](symbol){x1}<LSEP>[]

mbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){CramerV}<LSEP>[](symbol){x1}<LSEP>[](symbol){x1}<LSEP>[argument 2; litteral](logical){NA}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k2}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){k1}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc

block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k2}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k2}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){CramerV}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LSEP>[argument 2; litteral](logical){NA}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}<LEND>[assign](){<-}<LSEP>[](symbol){tschuprow.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){check}<LEND

[argument 2; litteral](logical){NA}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}<LEND>[assign](){<-}<LSEP>[](symbol){tschuprow.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){check}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ is not a data.frame}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.fram

(){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ is not a data.frame}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){check}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP

:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){x[, }<LSEP>[](symbol){k1}<LSEP>[argument 2; litteral](str){] is converted to a factor}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND

](symbol){k1}<LSEP>[argument 2; litteral](str){] is converted to a factor}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){assoc}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<L

mbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](sy

LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){TschuprowT}<LSEP>[](symbol){x1}<LSEP>[](symbol){x1}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k2}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){k1}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k2}<LEND>[statement 1; assign](){<-}<LSEP>[

ll](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k2}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k2}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){TschuprowT}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}<LEND>[assign](){<-}<LSEP>[](symbol){pearson.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[]

mbol){TschuprowT}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}<LEND>[assign](){<-}<LSEP>[](symbol){pearson.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){check}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ is not a data.frame}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](

D>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ is not a data.frame}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){check}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argume

){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){x[, }<LSEP>[](symbol){k1}<LSEP>[argument 2; litteral](str){] is converted to a factor}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](sym

l](str){x[, }<LSEP>[](symbol){k1}<LSEP>[argument 2; litteral](str){] is converted to a factor}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){assoc}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[]

ol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbo

D>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){ContCoef}<LSEP>[](symbol){x1}<LSEP>[](symbol){x1}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k2}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){k1}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol)

{}<LSEP>[](symbol){:}<LSEP>[](symbol){k1}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k2}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k2}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){ContCoef}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}<LEND>[assign](){<-

>[](symbol){k2}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){ContCoef}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}<LEND>[assign](){<-}<LSEP>[](symbol){phi.data.frame}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){check}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str

>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){substitute}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){ is not a data.frame}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){check}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block]()

e branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){x[, }<LSEP>[](symbol){k1}<LSEP>[argument 2; litteral](str){] is converted to a factor}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSE

e branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){x[, }<LSEP>[](symbol){k1}<LSEP>[argument 2; litteral](str){] is converted to a factor}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){assoc}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[ar

P>[](symbol){assoc}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){k1}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](sym

; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k1}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){Phi}<LSEP>[](symbol){x1}<LSEP>[](symbol){x1}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){k2}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){k1}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LS

ow](){for}<LSEP>[](symbol){k2}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){k1}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){k2}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k1}<LSEP>[](symbol){k2}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k2}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){Phi}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}

(){}<LSEP>[](symbol){[}<LSEP>[](symbol){assoc}<LSEP>[](symbol){k2}<LSEP>[](symbol){k1}<LEND>[call](){}<LSEP>[](symbol){Phi}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){assoc}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){warpArea}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){d}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.dtw}<LSEP>[](symbol){d}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){dtw object required}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ii}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stats}<LSEP>[](symbol){approx}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index2}<LEND>[argument 2; c

mbol){::}<LSEP>[](symbol){stats}<LSEP>[](symbol){approx}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index2}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){N}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dg}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){M}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){N}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){ad

ument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){M}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){N}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){ad}<LEND>[call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ii}<LSEP>[](symbol){y}<LEND>[](symbol){dg}<LEND>[statement 4; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){ad}<LEND>[assign](){<-}<LSEP>[](symbol){.localWarpingStretch}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){d}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){id1}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LS

){ad}<LEND>[assign](){<-}<LSEP>[](symbol){.localWarpingStretch}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){d}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){id1}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index1}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){id2}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index2}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){id2}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){id2}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){M}<LEND>[statement 3; call](){}<LS

t 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){id2}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){N}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){M}<LEND>[statement 3; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){id1}<LSEP>[](symbol){id2}<LEND>[assign](){<-}<LSEP>[](symbol){.localWarpingCost}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){d}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){localCostMatrix}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){A dtw object with keep.interna...}<LEND>[s

](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){localCostMatrix}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){A dtw object with keep.interna...}<LEND>[statement 1; call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){localCostMatrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index1}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index2}

LSEP>[](symbol){index1}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){d}<LSEP>[](symbol){index2}

[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){ada.formula}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){formula}<LSEP>[](symbol){data}<LSEP>[](symbol){...}<LSEP>[](symbol){subset}<LSEP>[](symbol){na.action}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){match.call}<LSEP>[argument 0; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){model}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){method}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){control}<LEND>[litteral](NULL){NULL}<

ol){model}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){method}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){control}<LEND>[litteral](NULL){NULL}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){y}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){parms}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){...}<LEND>[litteral](NULL){NULL}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call

all](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){parms}<LEND>[assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){...}<LEND>[litteral](NULL){NULL}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){cost}<LEND>[litteral](NULL){NULL}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){m}<LSEP>[](symbol){na.action}<LEND>[](symbol){na.action}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){model.frame}<LEND>[statement 6; assign](){<-}<LSEP>

ment 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){model.frame}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){eval}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[](symbol){parent.frame}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){Terms}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](str){terms}<LEND>[statement 8; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){model.extract}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](str){response}<LEND>[statement

1; litteral](str){terms}<LEND>[statement 8; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){model.extract}<LSEP>[](symbol){m}<LSEP>[argument 1; litteral](str){response}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){preds}<LEND>[call](){}<LSEP>[](symbol){attr}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){m}<LEND>[](symbol){terms}<LEND>[argument 1; litteral](str){term.labels}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){preds}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[s

term.labels}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){preds}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){vec}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){m}<LEND>[](symbol){preds}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){vec}<LEND>[statement 2; assign](){=}<LSE

ol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){m}<LEND>[](symbol){preds}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){vec}<LEND>[statement 2; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[](symbol){preds}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](sy

mbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){m}<LEND>[](symbol){preds}<LEND>[statement 11; assign](){=}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){ada.default}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){...}<LSEP>[](symbol){na.action}<LEND>[statement 12; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){res}<LSEP>[](symbol){terms}<LEND>[](symbol){Terms}<LEND>[statement 13; assign](){=}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 14; assign](){=}<LSEP>[variable; call

variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){res}<LSEP>[](symbol){terms}<LEND>[](symbol){Terms}<LEND>[statement 13; assign](){=}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 14; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cl}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.name}<LSEP>[argument 0; litteral](str){ada}<LEND>[statement 15; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){res}<LSEP>[](symbol){call}<LEND>[](symbol){cl}<LEND>[](symbol){res}

ymbol){res}<LSEP>[](symbol){call}<LEND>[](symbol){cl}<LEND>[](symbol){res}

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.refstocksurl}<LSEP>[litteral](str){https://api.twelvedata.com/stocks}<LEND>[assign](){<-}<LSEP>[](symbol){ref_stocks}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){sym}<LSEP>[](symbol){as}<LSEP>[](symbol){exchange}<LSEP>[](symbol){country}<LSEP>[](symbol){type}<LSEP>[](symbol){apikey}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){apikey}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){apikey}<LEND>[call](){}<LSEP>[](symbol){.get_apikey}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){as}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){as}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){type}<LEND>[c

n](){<-}<LSEP>[](symbol){apikey}<LEND>[call](){}<LSEP>[](symbol){.get_apikey}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){as}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){as}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){type}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){.refstocksurl}<LSEP>[argument 1; litteral](str){?}<LSEP>[argument 2; litteral](str){&apikey=}<LSEP>[](symbol){apikey}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sym}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](

key=}<LSEP>[](symbol){apikey}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sym}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&symbol=}<LSEP>[](symbol){sym}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){exchange}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&exchange=}<LSEP>[](symbol){exc

>[](symbol){!=}<LSEP>[](symbol){exchange}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&exchange=}<LSEP>[](symbol){exchange}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){country}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&country=}<LSEP>[](symbol){country}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](sym

ymbol){qry}<LSEP>[argument 1; litteral](str){&country=}<LSEP>[](symbol){country}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){qry}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){qry}<LSEP>[argument 1; litteral](str){&type=}<LSEP>[](symbol){type}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){accessed}<LEND>[call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[argument 1; litteral](str){UTC}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}

>[statement 8; assign](){<-}<LSEP>[](symbol){accessed}<LEND>[call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[argument 1; litteral](str){UTC}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RcppSimdJson}<LSEP>[](symbol){fload}<LEND>[](symbol){qry}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){as}<LSEP>[argument 1; litteral](str){raw}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){sym}<LEND>[argum

(str){raw}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){sym}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){res}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){res}<LEND>[](symbol){sym}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){res}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP

](symbol){sym}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){res}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){status}<LEND>[argument 1; litteral](str){ok}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){message}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){data}<LEND>[](symbol){dat}<LEND>

(symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){message}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){data}<LEND>[](symbol){dat}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[argument 0; litteral](str){rbind}<LSEP>[](symbol){dat}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){dat}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The API returned NULL. Try to ...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LS

ol){dat}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The API returned NULL. Try to ...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dat}<LSEP>[argument 1; litteral](str){accessed}<LEND>[](symbol){accessed}<LEND>[](symbol){dat}

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

[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.read.dart}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){filename}<LSEP>[](symbol){ind.metafile}<LSEP>[](symbol){recalc}<LSEP>[](symbol){mono.rm}<LSEP>[](symbol){nas}<LSEP>[](symbol){topskip}<LSEP>[](symbol){lastmetric}<LSEP>[](symbol){covfilename}<LSEP>[](symbol){probar}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[

l](){}<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

<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>[](sy

P>[litteral](real){2.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){probar}<LSEP>[litteral](logical){FALSE}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){pa

l flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){[ Build =}<LSEP>[](symbol){build}<LSEP>[argument 4; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[

t}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Starting}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ind.metafile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ind.metafile}<LSEP>[](symbol){covfilename}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){dout}<LEND>[call](){}<LSEP>[](symbol){utils.read.dart}<LSEP>[](symbol){filename}<LSEP>[](symbol){nas}<LSEP>[](symbol){topskip}<LSEP>[](symbol){lastmetric}<LSEP>[](symbol){verbose}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){glout}<LEND>[call](){}<LSEP>[](symbol){utils.dart2genlight}<LSEP>[](symbol){dout}<LSEP>[

](symbol){filename}<LSEP>[](symbol){nas}<LSEP>[](symbol){topskip}<LSEP>[](symbol){lastmetric}<LSEP>[](symbol){verbose}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){glout}<LEND>[call](){}<LSEP>[](symbol){utils.dart2genlight}<LSEP>[](symbol){dout}<LSEP>[](symbol){ind.metafile}<LSEP>[](symbol){probar}<LSEP>[](symbol){verbose}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Data read in. Please check ca...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){recalc.flags}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){AvgP

}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Data read in. Please check ca...}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){recalc.flags}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){AvgPIC}<LSEP>[argument 1; litteral](str){OneRatioRef}<LSEP>[argument 2; litteral](str){OneRatioSnp}<LSEP>[argument 3; litteral](str){PICRef}<LSEP>[argument 4; litteral](str){PICSnp}<LSEP>[argument 5; litteral](str){CallRate}<LSEP>[argument 6; litteral](str){maf}<LSEP>[argument 7; litteral](str){FreqHets}<LSEP>[argument 8; litteral](str){FreqHomRef}<LSEP>[argument 9; litteral](str){FreqHomSnp}<LSEP>[argument 10; litteral](str){monomorphs}<LSEP>[argument 11; litteral](str){OneRatio}<LSEP>[argument 12; litteral](s

f}<LSEP>[argument 7; litteral](str){FreqHets}<LSEP>[argument 8; litteral](str){FreqHomRef}<LSEP>[argument 9; litteral](str){FreqHomSnp}<LSEP>[argument 10; litteral](str){monomorphs}<LSEP>[argument 11; litteral](str){OneRatio}<LSEP>[argument 12; litteral](str){PIC}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){TRUE}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){recalc.flags}<LEND>[statement 12; assign](){<

me}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){TRUE}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){recalc.flags}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){recalc.flags}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[litteral](real){2.000000}<LEND>[statement 14; contro

<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[litteral](real){2.000000}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){rdepth}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; bl

D>[](symbol){loc.metrics}<LEND>[](symbol){rdepth}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Read depth calculated and ad...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){rdepth}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[

>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){glout}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){rdepth}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){glout}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){glout}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){called.ind}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){glout}<LEND>[argume