Datasets:

lanesket
/

r-asts

Dataset card Viewer Files Files and versions Community

Split (1)

raw · 367k rows

ast stringlengths 16 28.2M
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){matjeffreys}<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){jeffreys}<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}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){interpret.dstatis}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){nscore}<LSEP>[](symbol){moment}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){moment}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){all}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Since dad-4, moment='all' is n...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){moment}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){moment}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.dstatis}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){arg1 must be an object of clas...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){nscore}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){Since dad-4, nscore can only b...}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nscore}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){nscore}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){coor}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){scores}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){group.name}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){coor}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){coor}<LEND>[](symbol){group.name}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){matcoor}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){coor}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nscore}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 8; assign](){=}<LSEP>[](symbol){colnoms}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variables}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){colnoms}<LEND>[statement 10; assign](){=}<LSEP>[](symbol){matmoments}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){group.name}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 11; assign](){=}<LSEP>[](symbol){colNames}<LEND>[call](){}<LSEP>[](symbol){character}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[statement 12; call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){moment}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){moyL}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){means}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){matmoments}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){matmoments}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){moyL}<LEND>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){colNames}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){colNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){mean}<LSEP>[](symbol){colnoms}<LSEP>[argument 2; litteral](str){.}<LEND>[argument 2; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){covL}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variances}<LEND>[](symbol){diag}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){covL}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variances}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){matmoments}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){matmoments}<LEND>[argument 1; call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){covL}<LEND>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){colNames}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){colNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){sd}<LSEP>[](symbol){colnoms}<LSEP>[argument 2; litteral](str){.}<LEND>[argument 3; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){covL}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variances}<LEND>[](symbol){diag}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){covL}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variances}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){matmoments}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){matmoments}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){covL}<LEND>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){matmoments}<LEND>[](symbol){group.name}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){colNames}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){colNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){var}<LSEP>[](symbol){colnoms}<LSEP>[argument 2; litteral](str){.}<LEND>[argument 4; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){covL}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){variances}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){matcov}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){covL}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 2; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){2.000000}<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; assign](){=}<LSEP>[](symbol){nom.col.cov}<LEND>[call](){}<LSEP>[](symbol){factor}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){num.col.cov}<LEND>[call](){}<LSEP>[](symbol){factor}<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){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){num.col.cov.i}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){p}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LSEP>[](symbol){p}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){nom.col.cov.i}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){cov}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){colnoms}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){colnoms}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){p}<LEND>[argument 2; litteral](str){.}<LEND>[argument 2; litteral](str){.}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){num.col.cov}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){num.col.cov}<LSEP>[](symbol){num.col.cov.i}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){nom.col.cov}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){nom.col.cov}<LSEP>[](symbol){nom.col.cov.i}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){matmoments}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){matmoments}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matcov}<LSEP>[](symbol){}<LSEP>[](symbol){num.col.cov}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){colNames}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){colNames}<LSEP>[](symbol){nom.col.cov}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The covariances cannot be comp...}<LEND>[argument 5; block](){}<LSEP>[statement 0; 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; assign](){=}<LSEP>[](symbol){matcor}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){correlations}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 2; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){num.col.cor}<LEND>[call](){}<LSEP>[](symbol){factor}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){nom.col.cor}<LEND>[call](){}<LSEP>[](symbol){factor}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<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){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){num.col.cor.i}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){p}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LSEP>[](symbol){p}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){nom.col.cor.i}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){cor}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){colnoms}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){colnoms}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){p}<LEND>[argument 2; litteral](str){.}<LEND>[argument 2; litteral](str){.}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){num.col.cor}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){num.col.cor}<LSEP>[](symbol){num.col.cor.i}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){nom.col.cor}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){nom.col.cor}<LSEP>[](symbol){nom.col.cor.i}<LEND>[statement 4; assign](){=}<LSEP>[](symbol){matcor}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matcor}<LSEP>[](symbol){}<LSEP>[](symbol){num.col.cor}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){colNames}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){colNames}<LSEP>[](symbol){nom.col.cor}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){matmoments}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){matmoments}<LSEP>[](symbol){matcor}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The correlations cannot be com...}<LEND>[argument 6; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){skewnessL}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){skewness}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){matmoments}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){matmoments}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){skewnessL}<LEND>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){colNames}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){colNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){skewness}<LSEP>[](symbol){colnoms}<LSEP>[argument 2; litteral](str){.}<LEND>[argument 7; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){kurtosisL}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){kurtosis}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){matmoments}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){matmoments}<LEND>[argument 1; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){kurtosisL}<LEND>[argument 1; litteral](logical){TRUE}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){colNames}<LEND>[call](){}<LSEP>[](symbol){append}<LSEP>[](symbol){colNames}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){kurtosis}<LSEP>[](symbol){colnoms}<LSEP>[argument 2; litteral](str){.}<LEND>[statement 13; assign](){=}<LSEP>[](symbol){matmoments}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){matmoments}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 14; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){matmoments}<LEND>[](symbol){group.name}<LEND>[statement 15; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){matmoments}<LEND>[](symbol){colNames}<LEND>[statement 16; assign](){=}<LSEP>[](symbol){pearson.mat}<LEND>[call](){}<LSEP>[](symbol){cor}<LSEP>[](symbol){matmoments}<LSEP>[](symbol){matcoor}<LEND>[statement 17; assign](){=}<LSEP>[](symbol){spearman.mat}<LEND>[call](){}<LSEP>[](symbol){cor}<LSEP>[](symbol){matmoments}<LSEP>[](symbol){matcoor}<LSEP>[argument 2; litteral](str){spearman}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){dev.pdf}<LEND>[call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){.Device}<LSEP>[argument 1; litteral](str){pdf}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){matmoments}<LEND>[argument 1; litteral](real){9.000000}<LEND>[statement 19; control flow](){if}<LSEP>[](symbol){dev.pdf}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){matmoments}<LEND>[argument 1; litteral](str){graphs displayed. Consider pro...}<LEND>[statement 20; call](){}<LSEP>[](symbol){plotframes}<LSEP>[](symbol){matcoor}<LSEP>[](symbol){matmoments}<LSEP>[argument 2; litteral](real){10.000000}<LSEP>[](symbol){moment}<LEND>[statement 21; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Pearson correlations between s...}<LEND>[statement 22; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){pearson.mat}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 23; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Spearman correlations between ...}<LEND>[statement 24; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){spearman.mat}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 25; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){pearson.mat}<LSEP>[](symbol){spearman.mat}
[](){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}
[](){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...}
[](){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}
[](){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}
[](){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){$}<LSEP>[](symbol){D}<LSEP>[](symbol){fd}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RColorBrewer}<LSEP>[](symbol){brewer.pal}<LEND>[argument 0; litteral](real){8.000000}<LSEP>[argument 1; litteral](str){Blues}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 15; call](){}<LSEP>[](symbol){return}<LSEP>[argument 0; litteral](NULL){NULL}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){stopforstatus}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){response}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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}
[](){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}
[](){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}
[](){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; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<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){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){levels.name}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){j}<LSEP>[](symbol){vars.name}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){levels.name}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){levels.name}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){There are NAs in the folder}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){tab}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){xf}<LSEP>[](symbol){table}<LEND>[false branch; 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){group}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xf}<LSEP>[](symbol){}<LSEP>[](symbol){group.name}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){groups.name}<LEND>[call](){}<LSEP>[](symbol){levels}<LSEP>[](symbol){group}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xf}<LEND>[argument 1; 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 4; assign](){<-}<LSEP>[](symbol){vars.name}<LEND>[call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tab}<LEND>[call](){}<LSEP>[](symbol){by}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LSEP>[](symbol){table}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tab}<LEND>[](symbol){groups.name}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nomdim}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){xf}<LSEP>[](symbol){dimnames}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){identdim}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){nomdim}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){nomdim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LSEP>[](symbol){identdim}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){If xf is a list of arrays, all...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tab}<LSEP>[](symbol){xf}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){is.negative}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){xf}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){is.negative}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){All elements of xf must be arr...}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){nb.groups}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){tab}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){groups.name}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tab}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){vars.name}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){dimnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tab}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){levels.name}<LEND>[call](){}<LSEP>[](symbol){dimnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tab}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){nb.vars}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){vars.name}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dims}<LEND>[call](){}<LSEP>[](symbol){dim}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tab}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){freq}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){tab}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){x}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){distance}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){distance}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){distance}<LSEP>[argument 1; litteral](str){l1}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){distance}<LSEP>[litteral](str){lp}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){p}<LSEP>[litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){distance.printing}<LSEP>[litteral](str){l1}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){distance}<LSEP>[argument 1; litteral](str){l2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){distance}<LSEP>[litteral](str){lp}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){p}<LSEP>[litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){distance.printing}<LSEP>[litteral](str){l2}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){distance}<LSEP>[argument 1; litteral](str){lp}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){p}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){p}<LSEP>[litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){distance.printing}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){lp with p =}<LSEP>[](symbol){p}<LEND>[statement 9; call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){distance}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matdist}<LEND>[call](){}<LSEP>[](symbol){matddlppar}<LSEP>[](symbol){freq}<LSEP>[](symbol){p}<LEND>[argument 2; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matdist}<LEND>[call](){}<LSEP>[](symbol){matddhellingerpar}<LSEP>[](symbol){freq}<LEND>[argument 3; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matdist}<LEND>[call](){}<LSEP>[](symbol){matddchisqsympar}<LSEP>[](symbol){freq}<LEND>[argument 4; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matdist}<LEND>[call](){}<LSEP>[](symbol){matddjeffreyspar}<LSEP>[](symbol){freq}<LEND>[argument 5; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){matdist}<LEND>[call](){}<LSEP>[](symbol){matddjensenpar}<LSEP>[](symbol){freq}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.finite}<LSEP>[](symbol){matdist}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xclust}<LEND>[call](){}<LSEP>[](symbol){hclust}<LSEP>[](symbol){matdist}<LSEP>[](symbol){method.hclust}<LSEP>[argument 2; litteral](NULL){NULL}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){matdist}<LSEP>[](symbol){xclust}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){results}<LEND>[litteral](str){hclustdd}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){results}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Some distances between groups ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){matdist}<LSEP>[argument 1; litteral](NULL){NULL}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){results}<LEND>[litteral](str){hclustdd}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){results}
[](){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}
[](){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){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){col}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){col}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){col}<LSEP>[litteral](str){#EE6677FF}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){base}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){k}<LSEP>[litteral](real){1.000000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){base}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){10}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){log}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){log}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){base}<LSEP>[litteral](str){e}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){is_log}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){base}<LSEP>[litteral](str){e}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){base}<LSEP>[litteral](str){10}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){log}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){xlab}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){xlab}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){xlab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlab}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){e}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){log(Predictor)}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){Predictor}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){ylab}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){ylab}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ylab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ylab}<LSEP>[litteral](str){Response}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){theta}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){coefficients}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){alpha}<LSEP>[litteral](real){0.000000}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){beta}<LSEP>[litteral](real){1.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){phi}<LSEP>[litteral](real){0.000000}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mean_function}<LEND>[argument 1; litteral](str){logistic2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){alpha}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){beta}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){phi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){phi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){xv}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){model}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){yv}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){model}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){wv}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){weights}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){idx}<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){is.na}<LSEP>[](symbol){yv}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){xv}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){wv}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){wv}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){idx}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){yv}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){yv}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){yv}<LSEP>[](symbol){idx}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xv}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xv}<LSEP>[](symbol){idx}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){wv}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){wv}<LSEP>[](symbol){idx}<LEND>[statement 26; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){is_log}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xv}<LEND>[call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){xv}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){xlim}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){xlim}<LEND>[statement 28; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){xlim}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlim}<LEND>[call](){}<LSEP>[](symbol){extendrange}<LSEP>[](symbol){xv}<LSEP>[argument 1; litteral](real){0.080000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){phi}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){phi}<LSEP>[argument 1; litteral](real){50.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){phi}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){phi}<LSEP>[argument 1; litteral](real){50.000000}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){ylim}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){ylim}<LEND>[statement 30; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ylim}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ylim}<LEND>[call](){}<LSEP>[](symbol){extendrange}<LSEP>[](symbol){yv}<LSEP>[argument 1; litteral](real){0.080000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){alpha}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){alpha}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){beta}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){beta}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 3; 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){ylim}<LSEP>[argument 1; litteral](real){1.000000}<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){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[litteral](real){0.000000}<LEND>[statement 4; 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){ylim}<LSEP>[argument 1; litteral](real){2.000000}<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){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](real){500.000000}<LEND>[statement 32; assign](){<-}<LSEP>[](symbol){mu}<LEND>[call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){x}<LSEP>[](symbol){xx}<LSEP>[](symbol){theta}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){level}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){level}<LEND>[statement 34; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){level}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){level}<LSEP>[litteral](real){0.950000}<LEND>[statement 35; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){level}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){level}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){qchisq}<LSEP>[](symbol){level}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){estimated}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cv}<LEND>[call](){}<LSEP>[](symbol){curve_variance}<LSEP>[](symbol){x}<LSEP>[](symbol){xx}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cs}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){q}<LSEP>[](symbol){cv}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){upper_bound}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){mu}<LSEP>[](symbol){cs}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){lower_bound}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){mu}<LSEP>[](symbol){cs}<LEND>[statement 36; 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){x_axis_ticks}<LEND>[call](){}<LSEP>[](symbol){pretty}<LSEP>[](symbol){xlim}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x_axis_labels}<LSEP>[litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlim}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xlim}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xv}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xv}<LSEP>[](symbol){k}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xx}<LSEP>[](symbol){k}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xv}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xv}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){xv}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){x_axis_ticks}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LEND>[argument 2; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x2}<LSEP>[](symbol){x1}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){x_axis_labels}<LSEP>[litteral](logical){FALSE}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){\|\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){10}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x_axis_labels}<LEND>[call](){}<LSEP>[](symbol){str2expression}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){^}<LSEP>[](symbol){x_axis_ticks}<LSEP>[argument 3; litteral](str){}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){x_axis_minor}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){10}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){log10}<LEND>[argument 0; call](){}<LSEP>[](symbol){pretty}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_ticks}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){9.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_ticks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){log2}<LEND>[argument 0; call](){}<LSEP>[](symbol){pretty}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_ticks}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){9.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_ticks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){x_axis_minor}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_minor}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x_axis_minor}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){x_axis_minor}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){outer}<LSEP>[](symbol){x_axis_minor}<LSEP>[](symbol){x_axis_ticks}<LSEP>[](symbol){+}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){x_axis_minor}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_minor}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){x_axis_minor}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){x_axis_minor}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 37; call](){}<LSEP>[](symbol){dev.hold}<LEND>[statement 38; call](){}<LSEP>[](symbol){plot.default}<LSEP>[](symbol){xlim}<LSEP>[](symbol){ylim}<LSEP>[argument 2; litteral](str){n}<LSEP>[](symbol){xlim}<LSEP>[](symbol){ylim}<LSEP>[](symbol){xlab}<LSEP>[](symbol){ylab}<LSEP>[argument 7; litteral](logical){FALSE}<LEND>[statement 39; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){x_axis_ticks}<LSEP>[](symbol){x_axis_labels}<LEND>[statement 40; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){e}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){x_axis_minor}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[argument 3; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){tcl}<LEND>[argument 1; litteral](real){0.500000}<LEND>[statement 41; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){pretty}<LSEP>[](symbol){ylim}<LEND>[statement 42; call](){}<LSEP>[](symbol){box}<LEND>[statement 43; call](){}<LSEP>[](symbol){points}<LSEP>[](symbol){xv}<LSEP>[](symbol){yv}<LSEP>[](symbol){col}<LEND>[statement 44; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){xx}<LSEP>[](symbol){mu}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[](symbol){col}<LEND>[statement 45; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){level}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){level}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xci}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){xx}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){xx}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){yci}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){upper_bound}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){lower_bound}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cc}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){col2rgb}<LSEP>[](symbol){col}<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 46; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){\|\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mean_function}<LEND>[argument 1; litteral](str){logistic2}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mean_function}<LEND>[argument 1; litteral](str){logistic4}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){x}<LSEP>[](symbol){phi}<LSEP>[](symbol){theta}<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}<LSEP>[](symbol){col}<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}<LSEP>[](symbol){col}<LEND>[statement 47; 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 48; assign](){<-}<LSEP>[](symbol){legend_labels}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){legend}<LEND>[statement 49; 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){$}<LSEP>[](symbol){x}<LSEP>[](symbol){mean_function}<LEND>[statement 50; call](){}<LSEP>[](symbol){legend}<LSEP>[](symbol){location}<LSEP>[](symbol){col}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](str){white}<LSEP>[](symbol){legend_labels}<LEND>[statement 51; call](){}<LSEP>[](symbol){dev.flush}<LEND>[statement 52; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](NULL){NULL}<LEND>[assign](){<-}<LSEP>[](symbol){plot.drdalist}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n_curves}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){n_curves}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){plot.drda}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](integer){1}<LEND>[](symbol){...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){M}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){is_log}<LEND>[call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){y}<LSEP>[](symbol){is_log}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){dotargs}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){col}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){col}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){col}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){col}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){M}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){#EE6677FF}<LSEP>[argument 1; litteral](str){#4477AAFF}<LSEP>[argument 2; litteral](str){#228833FF}<LSEP>[argument 3; litteral](str){#AA3377FF}<LSEP>[argument 4; litteral](str){#66CCEEFF}<LSEP>[argument 5; litteral](str){#CCBB44FF}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){#CC6677FF}<LSEP>[argument 1; litteral](str){#332288FF}<LSEP>[argument 2; litteral](str){#117733FF}<LSEP>[argument 3; litteral](str){#882255FF}<LSEP>[argument 4; litteral](str){#88CCEEFF}<LSEP>[argument 5; litteral](str){#999933FF}<LSEP>[argument 6; litteral](str){#AA4499FF}<LSEP>[argument 7; litteral](str){#44AA99FF}<LSEP>[argument 8; litteral](str){#DDCC77FF}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){col}<LEND>[](symbol){M}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){col}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){col}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](str){#000000FF}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){M}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){col}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){base}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){k}<LSEP>[litteral](real){1.000000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){base}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){10}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){log}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){log}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){base}<LSEP>[litteral](str){e}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){is_log}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){base}<LSEP>[litteral](str){e}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){base}<LSEP>[litteral](str){10}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){log}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){xlab}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){xlab}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){xlab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlab}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){e}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](str){log(Predictor)}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](str){Predictor}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){ylab}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){ylab}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ylab}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ylab}<LSEP>[litteral](str){Response}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){alpha}<LSEP>[litteral](real){0.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){beta}<LSEP>[litteral](real){1.000000}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){eta}<LSEP>[litteral](real){0.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){phi_min}<LSEP>[litteral](real){0.000000}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){phi_max}<LSEP>[litteral](real){0.000000}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){xv}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[argument 0; litteral](str){list}<LSEP>[](symbol){M}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){yv}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[argument 0; litteral](str){list}<LSEP>[](symbol){M}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){wv}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[argument 0; litteral](str){list}<LSEP>[](symbol){M}<LEND>[statement 23; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){M}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){theta}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){coefficients}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){mean_function}<LEND>[argument 1; litteral](str){logistic2}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){alpha}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){alpha}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){beta}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){beta}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](symbol){phi_min}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){phi_min}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){eta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){eta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](symbol){phi_max}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){phi_max}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){eta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eta}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){eta}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){phi_min}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){phi_min}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){phi_max}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){phi_max}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){theta}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xv}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){model}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){yv}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){model}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){wv}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){weights}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){idx}<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){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){yv}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xv}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){wv}<LSEP>[](symbol){i}<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){wv}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){idx}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){yv}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){yv}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){yv}<LSEP>[](symbol){i}<LEND>[](symbol){idx}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xv}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xv}<LSEP>[](symbol){i}<LEND>[](symbol){idx}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){wv}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){wv}<LSEP>[](symbol){i}<LEND>[](symbol){idx}<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){x}<LSEP>[](symbol){i}<LEND>[](symbol){is_log}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xv}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xv}<LSEP>[](symbol){i}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){xlim}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){xlim}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){xlim}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlim}<LEND>[call](){}<LSEP>[](symbol){extendrange}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){xv}<LEND>[argument 1; litteral](real){0.080000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){phi_min}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){phi_min}<LSEP>[argument 1; litteral](real){50.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){phi_max}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){phi_max}<LSEP>[argument 1; litteral](real){50.000000}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){ylim}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){ylim}<LEND>[statement 27; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){ylim}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ylim}<LEND>[call](){}<LSEP>[](symbol){extendrange}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){yv}<LEND>[argument 1; litteral](real){0.080000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){alpha}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){alpha}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){beta}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){beta}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 3; 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){ylim}<LSEP>[argument 1; litteral](real){1.000000}<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){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[litteral](real){0.000000}<LEND>[statement 4; 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){ylim}<LSEP>[argument 1; litteral](real){2.000000}<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){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){ylim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[litteral](real){1.000000}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](real){500.000000}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){mu}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){x}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){y}<LSEP>[](symbol){xx}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){y}<LSEP>[](symbol){coefficients}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){level}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){level}<LEND>[statement 31; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){level}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){level}<LSEP>[litteral](real){0.950000}<LEND>[statement 32; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){level}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){level}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){upper_bound}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[argument 0; litteral](str){list}<LSEP>[](symbol){M}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lower_bound}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[argument 0; litteral](str){list}<LSEP>[](symbol){M}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){M}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){qchisq}<LSEP>[](symbol){level}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){estimated}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cv}<LEND>[call](){}<LSEP>[](symbol){curve_variance}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){i}<LEND>[](symbol){xx}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cs}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){q}<LSEP>[](symbol){cv}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){upper_bound}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){mu}<LSEP>[](symbol){i}<LEND>[](symbol){cs}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){mu}<LSEP>[](symbol){i}<LEND>[](symbol){cs}<LEND>[statement 33; 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){x_axis_ticks}<LEND>[call](){}<LSEP>[](symbol){pretty}<LSEP>[](symbol){xlim}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x_axis_labels}<LSEP>[litteral](logical){TRUE}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlim}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xlim}<LSEP>[](symbol){k}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xv}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){xv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){y}<LSEP>[](symbol){k}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){xx}<LSEP>[](symbol){k}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){xv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){xv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[argument 2; litteral](real){0.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){x_axis_ticks}<LEND>[call](){}<LSEP>[](symbol){seq}<LSEP>[](symbol){x1}<LSEP>[](symbol){x2}<LEND>[argument 2; call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x2}<LSEP>[](symbol){x1}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){x_axis_labels}<LSEP>[litteral](logical){FALSE}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){\|\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){10}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){2}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x_axis_labels}<LEND>[call](){}<LSEP>[](symbol){str2expression}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){^}<LSEP>[](symbol){x_axis_ticks}<LSEP>[argument 3; litteral](str){}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){x_axis_minor}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){10}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){log10}<LEND>[argument 0; call](){}<LSEP>[](symbol){pretty}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_ticks}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){9.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_ticks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){log2}<LEND>[argument 0; call](){}<LSEP>[](symbol){pretty}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_ticks}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){9.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_ticks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){x_axis_minor}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_minor}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x_axis_minor}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){x_axis_minor}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){outer}<LSEP>[](symbol){x_axis_minor}<LSEP>[](symbol){x_axis_ticks}<LSEP>[](symbol){+}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){x_axis_minor}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x_axis_minor}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){x_axis_minor}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){x_axis_minor}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xlim}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 34; call](){}<LSEP>[](symbol){dev.hold}<LEND>[statement 35; call](){}<LSEP>[](symbol){plot.default}<LSEP>[](symbol){xlim}<LSEP>[](symbol){ylim}<LSEP>[argument 2; litteral](str){n}<LSEP>[](symbol){xlim}<LSEP>[](symbol){ylim}<LSEP>[](symbol){xlab}<LSEP>[](symbol){ylab}<LSEP>[argument 7; litteral](logical){FALSE}<LEND>[statement 36; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){x_axis_ticks}<LSEP>[](symbol){x_axis_labels}<LEND>[statement 37; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){e}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){x_axis_minor}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[argument 3; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](str){tcl}<LEND>[argument 1; litteral](real){0.500000}<LEND>[statement 38; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){pretty}<LSEP>[](symbol){ylim}<LEND>[statement 39; call](){}<LSEP>[](symbol){box}<LEND>[statement 40; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){M}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){points}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xv}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){yv}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){col}<LSEP>[](symbol){i}<LEND>[statement 1; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){xx}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){mu}<LSEP>[](symbol){i}<LEND>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){col}<LSEP>[](symbol){i}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){level}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){level}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xci}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){xx}<LEND>[argument 1; call](){}<LSEP>[](symbol){rev}<LSEP>[](symbol){xx}<LEND>[statement 1; 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){$}<LSEP>[](symbol){y}<LSEP>[](symbol){mean_function}<LEND>[argument 2; litteral](str){a}<LEND>[statement 44; call](){}<LSEP>[](symbol){legend}<LSEP>[](symbol){location}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){col}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M}<LEND>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](str){white}<LSEP>[](symbol){legend_labels}<LEND>[statement 45; call](){}<LSEP>[](symbol){dev.flush}<LEND>[statement 46; call](){}<LSEP>[](symbol){invisible}<LSEP>[argument 0; litteral](NULL){NULL}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plot.ata}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){conditem}<LSEP>[](symbol){useconst}<LSEP>[](symbol){itemorder}<LSEP>[](symbol){itemlab}<LSEP>[](symbol){useitemlab}<LSEP>[](symbol){together}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){oldpar}<LEND>[call](){}<LSEP>[](symbol){par}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[statement 1; call](){}<LSEP>[](symbol){on.exit}<LEND>[argument 0; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){oldpar}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){names_const}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){itemorder}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Provided item order does not r...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){useorder}<LSEP>[](symbol){itemorder}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){useorder}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){useitemlab}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){itemlab}<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){itemlab}<LEND>[](symbol){nI}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The number of provided item la...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){itemlab}<LEND>[](symbol){nI}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The number of provided item la...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){itemlabuse}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){itemlab}<LSEP>[](symbol){useorder}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){useitemlab}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){itemlab}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){itemlabuse}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){final_ids}<LEND>[](symbol){useorder}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){itemlabuse}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<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){conditem}<LEND>[](symbol){nI}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The number of provided conditi...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){conditem}<LEND>[](symbol){nI}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The number of provided conditi...}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){nC}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){isTRUE}<LSEP>[](symbol){together}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Large number of constraints sh...}<LEND>[statement 11; 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>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){useconst}<LEND>[](symbol){nC}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){More visualizations requested ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){useconst}<LSEP>[](symbol){names_const}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Identified constraint(s) not i...}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){cumulative}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 13; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nC}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){constcumtemp}<LEND>[call](){}<LSEP>[](symbol){c}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){constcumtemp}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){constcumtemp}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){useorder}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){j}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){names_const}<LSEP>[](symbol){i}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cumulative}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){constcumtemp}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){names_const}<LSEP>[](symbol){i}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){x}<LEND>[](symbol){method}<LEND>[argument 1; litteral](str){wdm}<LEND>[true branch; block](){}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){x}<LEND>[](symbol){method}<LEND>[argument 1; litteral](str){lp}<LEND>[true branch; block](){}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){together}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<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){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){plotnC}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pcub}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){4.500000}<LSEP>[argument 1; litteral](real){4.500000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){o}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 5; litteral](str){Item}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){pcub}<LEND>[argument 8; litteral](real){20.000000}<LSEP>[argument 9; litteral](real){2.000000}<LSEP>[argument 10; litteral](str){n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){b}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 5; litteral](str){Item}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){pcub}<LEND>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){3.000000}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<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 2; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[](symbol){itemlabuse}<LEND>[statement 3; call](){}<LSEP>[](symbol){abline}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){darkgreen}<LSEP>[argument 1; litteral](str){red3}<LEND>[argument 2; litteral](real){3.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){4.500000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){o}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 5; litteral](str){}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){pcub}<LEND>[argument 8; litteral](real){20.000000}<LSEP>[argument 9; litteral](real){2.000000}<LSEP>[argument 10; litteral](str){n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){b}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 5; litteral](str){}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){pcub}<LEND>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){3.000000}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<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 2; call](){}<LSEP>[](symbol){abline}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){darkgreen}<LSEP>[argument 1; litteral](str){red3}<LEND>[argument 2; litteral](real){3.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){j}<LSEP>[](symbol){plotnC}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){4.500000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){o}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 5; litteral](str){Item}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){pcub}<LEND>[argument 8; litteral](real){20.000000}<LSEP>[argument 9; litteral](real){2.000000}<LSEP>[argument 10; litteral](str){n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){b}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 5; litteral](str){Item}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){pcub}<LEND>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){3.000000}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<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 2; call](){}<LSEP>[](symbol){abline}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){darkgreen}<LSEP>[argument 1; litteral](str){red3}<LEND>[argument 2; litteral](real){3.000000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){j}<LSEP>[](symbol){plotnC}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){4.500000}<LSEP>[argument 1; litteral](real){4.500000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){o}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 5; litteral](str){Item}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){pcub}<LEND>[argument 8; litteral](real){20.000000}<LSEP>[argument 9; litteral](real){2.000000}<LSEP>[argument 10; litteral](str){n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){b}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 5; litteral](str){Item}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){pcub}<LEND>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){3.000000}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<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 2; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[](symbol){itemlabuse}<LEND>[statement 3; call](){}<LSEP>[](symbol){abline}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){darkgreen}<LSEP>[argument 1; litteral](str){red3}<LEND>[argument 2; litteral](real){3.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){plotnC}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pcub}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){4.500000}<LSEP>[argument 1; litteral](real){4.500000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){o}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 5; litteral](str){Item}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){pcub}<LEND>[argument 8; litteral](real){20.000000}<LSEP>[argument 9; litteral](real){2.000000}<LSEP>[argument 10; litteral](str){n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){b}<LSEP>[argument 3; litteral](real){2.000000}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 5; litteral](str){Item}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){pcub}<LEND>[argument 8; litteral](real){1.000000}<LSEP>[argument 9; litteral](real){3.000000}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<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 3; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[](symbol){itemlabuse}<LEND>[statement 4; call](){}<LSEP>[](symbol){abline}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){darkgreen}<LSEP>[argument 1; litteral](str){red3}<LEND>[argument 2; litteral](real){3.000000}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){together}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<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){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){rep}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){plotnC}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pcdv}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){4.500000}<LSEP>[argument 1; litteral](real){4.500000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){o}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){20.000000}<LSEP>[argument 5; litteral](real){2.000000}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 9; litteral](str){Item}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[](symbol){itemlabuse}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){b}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){3.000000}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 9; litteral](str){Item}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[](symbol){itemlabuse}<LEND>[statement 2; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){plotnC}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){4.500000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){o}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){20.000000}<LSEP>[argument 5; litteral](real){2.000000}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 9; litteral](str){Item}<LSEP>[argument 10; litteral](str){n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){b}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){3.000000}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 9; litteral](str){Item}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){j}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){j}<LSEP>[](symbol){plotnC}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){4.500000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){o}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){20.000000}<LSEP>[argument 5; litteral](real){2.000000}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 9; litteral](str){Item}<LSEP>[argument 10; litteral](str){n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){b}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){3.000000}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 9; litteral](str){Item}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){j}<LSEP>[](symbol){plotnC}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){4.500000}<LSEP>[argument 1; litteral](real){4.500000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){o}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){20.000000}<LSEP>[argument 5; litteral](real){2.000000}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 9; litteral](str){Item}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[](symbol){itemlabuse}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){b}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){3.000000}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 9; litteral](str){Item}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[](symbol){itemlabuse}<LEND>[statement 2; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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 2; call](){}<LSEP>[](symbol){layout}<LEND>[argument 0; call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){plotnC}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pcdv}<LEND>[call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){evaluation}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){cumulative}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){4.500000}<LSEP>[argument 1; litteral](real){4.500000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){conditem}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){o}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){20.000000}<LSEP>[argument 5; litteral](real){2.000000}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 9; litteral](str){Item}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[](symbol){itemlabuse}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){b}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[argument 4; litteral](real){1.000000}<LSEP>[argument 5; litteral](real){3.000000}<LSEP>[argument 6; litteral](str){}<LEND>[argument 7; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[](symbol){pcdv}<LEND>[argument 8; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){plotconst}<LSEP>[](symbol){j}<LEND>[argument 9; litteral](str){Item}<LSEP>[argument 10; litteral](str){n}<LEND>[statement 1; call](){}<LSEP>[](symbol){axis}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[](symbol){itemlabuse}<LEND>[statement 2; call](){}<LSEP>[](symbol){text}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nI}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){included}<LEND>[](symbol){useorder}<LEND>[argument 2; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.filter.secondaries}<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; call](){}<LSEP>[](symbol){stop}<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>[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; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){best}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){random}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: method must be sp...}<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; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Total number of SNP loci:}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){best}<LEND>[true branch; block](){}<LSEP>[statement 0; 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){ Selecting one SNP per sequen...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){loc.order}<LEND>[call](){}<LSEP>[](symbol){order}<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){AlleleID}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){RepAvg}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){AvgPIC}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){loc.order}<LEND>[statement 3; 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){loc.order}<LSEP>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; 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){ Selecting one SNP per sequen...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){n}<LEND>[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){AlleleID}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){index}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){10000.000000}<LEND>[](symbol){n}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){index}<LEND>[statement 4; 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>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){index}<LEND>[](symbol){}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<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){AlleleID}<LEND>[argument 1; litteral](str){\\\|}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){a}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](logical){TRUE}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){b}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 13; 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>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){b}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[](symbol){}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){b}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nsec}<LSEP>[litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nsec}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){b}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Number of secondaries:}<LSEP>[](symbol){nsec}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Number of loci after secon...}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){duplicated}<LSEP>[](symbol){b}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){nh}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){history}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){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 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}
[](){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){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){dtw}<LSEP>[argument 0; litteral](logical){TRUE}<LSEP>[](symbol){...}<LEND>[](symbol){distance}
[](){expression}<LSEP>[litteral](NULL){NULL}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){DRAT_ARCHIVE_SUB_DIR}<LSEP>[litteral](str){Archive}<LEND>[assign](){<-}<LSEP>[](symbol){DRAT_BINARY_TYPES}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){mac.binary}<LSEP>[argument 1; litteral](str){mac.binary.el-capitan}<LSEP>[argument 2; litteral](str){mac.binary.mavericks}<LSEP>[argument 3; litteral](str){win.binary}<LEND>[assign](){<-}<LSEP>[](symbol){DRAT_BOTH_TYPES}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){source}<LSEP>[argument 1; litteral](str){mac.binary}<LSEP>[argument 2; litteral](str){mac.binary.el-capitan}<LSEP>[argument 3; litteral](str){mac.binary.mavericks}<LSEP>[argument 4; litteral](str){win.binary}<LEND>[assign](){<-}<LSEP>[](symbol){DRAT_VERSION_REGEX}<LSEP>[litteral](str){[0-9]\\.[0-9]$}<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}
[](){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; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xf}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){j.group}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){xf}<LSEP>[argument 1; litteral](str){keys}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){j.group}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){j.group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){j.group}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){classe}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){xf}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){xf}<LSEP>[argument 1; litteral](str){keys}<LEND>[](symbol){class.var}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 7; 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){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; 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){j}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){group}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){nb.groups}<LEND>[call](){}<LSEP>[](symbol){nlevels}<LSEP>[](symbol){group}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){group.name}<LEND>[call](){}<LSEP>[](symbol){levels}<LSEP>[](symbol){group}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){nb.classe}<LEND>[call](){}<LSEP>[](symbol){nlevels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){classe.name}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){identical}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The names of the groups in the...}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){factor}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 17; control flow](){for}<LSEP>[](symbol){n.x}<LEND>[range; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n.x}<LEND>[argument 2; litteral](str){classe}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){n.x}<LEND>[argument 2; litteral](real){2.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){tabgr}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){table}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){tabcl}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){q}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){table}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){classe}<LEND>[argument 1; call](){}<LSEP>[](symbol){nlevels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 21; call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){crit}<LEND>[argument 1; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){n.x}<LEND>[range; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){distances}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n.x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){n.cl}<LEND>[range; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){distances}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){n.x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){n.cl}<LEND>[argument 2; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tabcl.tmp}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabcl}<LSEP>[](symbol){n.cl}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){indcl}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){n.cl}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n.x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){tabcl.tmp}<LEND>[call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){indcl}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){q}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){n.x}<LSEP>[](symbol){n.cl}<LEND>[call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){distance}<LEND>[argument 1; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){ddchisqsympar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 4; call](){}<LSEP>[](symbol){ddhellingerpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 5; call](){}<LSEP>[](symbol){ddjeffreyspar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 6; call](){}<LSEP>[](symbol){ddjensenpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 7; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[](symbol){p}<LEND>[argument 2; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){n.x}<LEND>[range; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){distances}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n.x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){n.cl}<LEND>[range; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){distances}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){indcl}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){n.cl}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){n.x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){Tj}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){indcl}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){x.cl}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){indcl}<LEND>[argument 2; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){q}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tabcl.tmp}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){Reduce}<LSEP>[argument 0; litteral](str){+}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){x.cl}<LEND>[](symbol){Tj}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){n.x}<LSEP>[](symbol){n.cl}<LEND>[call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){distance}<LEND>[argument 1; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){ddchisqsympar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 4; call](){}<LSEP>[](symbol){ddhellingerpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 5; call](){}<LSEP>[](symbol){ddjeffreyspar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 6; call](){}<LSEP>[](symbol){ddjensenpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 7; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[](symbol){p}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nomdim}<LEND>[call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){xf}<LSEP>[](symbol){dimnames}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){identdim}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){nomdim}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){identical}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){nomdim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LSEP>[](symbol){identdim}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){If xf is a list of arrays, all...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){is.negative}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){xf}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){is.negative}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){All elements of xf must be arr...}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){classe}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){class.var}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){group}<LSEP>[argument 1; litteral](str){class}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){xf}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){distances}<LEND>[call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){class.var}<LEND>[argument 1; call](){}<LSEP>[](symbol){nlevels}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){class.var}<LSEP>[](symbol){class}<LEND>[argument 2; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){class.var}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){class.var}<LSEP>[](symbol){class}<LEND>[statement 8; call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){crit}<LEND>[argument 1; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){n.x}<LEND>[range; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){distances}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){n.cl}<LEND>[range; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){distances}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x.cl}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){class.var}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){class.var}<LSEP>[](symbol){class}<LEND>[](symbol){n.cl}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){class.var}<LSEP>[](symbol){group}<LEND>[](symbol){n.x}<LEND>[argument 2; litteral](str){group}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){indcl}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tabgr}<LEND>[](symbol){x.cl}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){Tj}<LEND>[call](){}<LSEP>[](symbol){Reduce}<LSEP>[](symbol){sum}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){indcl}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tabcl.tmp}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){Reduce}<LSEP>[argument 0; litteral](str){+}<LEND>[argument 1; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){indcl}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){x}<LEND>[](symbol){Tj}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){n.x}<LSEP>[](symbol){n.cl}<LEND>[call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){distance}<LEND>[argument 1; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){ddchisqsympar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 4; call](){}<LSEP>[](symbol){ddhellingerpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 5; call](){}<LSEP>[](symbol){ddjeffreyspar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 6; call](){}<LSEP>[](symbol){ddjensenpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 7; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[](symbol){p}<LEND>[argument 2; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){n.x}<LEND>[range; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){distances}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){n.cl}<LEND>[range; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){distances}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x.cl}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){class.var}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){class.var}<LSEP>[](symbol){class}<LEND>[](symbol){n.cl}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){class.var}<LSEP>[](symbol){group}<LEND>[](symbol){n.x}<LEND>[argument 2; litteral](str){group}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){indcl}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tabgr}<LEND>[](symbol){x.cl}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){Tj}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){indcl}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){tabcl.tmp}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){Reduce}<LSEP>[argument 0; litteral](str){+}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){indcl}<LEND>[](symbol){Tj}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){distances}<LSEP>[](symbol){n.x}<LSEP>[](symbol){n.cl}<LEND>[call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){distance}<LEND>[argument 1; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){ddchisqsympar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 4; call](){}<LSEP>[](symbol){ddhellingerpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 5; call](){}<LSEP>[](symbol){ddjeffreyspar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 6; call](){}<LSEP>[](symbol){ddjensenpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LEND>[argument 7; call](){}<LSEP>[](symbol){ddlppar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabgr}<LSEP>[](symbol){n.x}<LEND>[](symbol){tabcl.tmp}<LSEP>[](symbol){p}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){group.calc}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){distances}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){which.min}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){group.calc}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){group.calc}<LEND>[argument 1; litteral](str){.}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[](symbol){head}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){misclass}<LSEP>[](symbol){classe}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){misclass}<LEND>[argument 1; litteral](real){2.000000}<LEND>[litteral](str){prior.class}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){misclass}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classe}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){lev.class}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){misclass}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){misclass}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){misclass}<LEND>[argument 1; call](){}<LSEP>[](symbol){factor}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){lev.class}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){misclass}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){group.calc}<LEND>[argument 2; litteral](str){predicted.class}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lev.class}<LSEP>[](symbol){group.calc}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){misclass}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){misclass}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){misclass}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){misclass}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){alloc.per.classe}<LEND>[call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){misclass}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){inv.distances}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){distances}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){sum.inv.distances}<LEND>[call](){}<LSEP>[](symbol){rowSums}<LSEP>[](symbol){inv.distances}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){prox}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){inv.distances}<LSEP>[](symbol){sum.inv.distances}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){classe.ratio}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){diag}<LSEP>[](symbol){alloc.per.classe}<LEND>[argument 1; call](){}<LSEP>[](symbol){rowSums}<LSEP>[](symbol){alloc.per.classe}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){classe.ratio}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){classe.ratio}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){misclass.per.classe}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){100.000000}<LSEP>[](symbol){classe.ratio}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){distance}<LSEP>[argument 1; litteral](str){lp}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){distance}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){lp with p =}<LSEP>[](symbol){p}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){distance}<LSEP>[](symbol){misclass}<LSEP>[](symbol){alloc.per.classe}<LSEP>[](symbol){misclass.per.classe}<LEND>[argument 4; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){misclass}<LSEP>[](symbol){misclassed}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){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}
[](){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}
[](){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}
[](){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}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){as.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){as.folder}
[](){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; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){w}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){missing or negative weights no...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){w_zero}<LEND>[call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){w}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){w_zero}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){w_positive}<LEND>[call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){w_zero}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){w_positive}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){w_positive}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LSEP>[](symbol){w_positive}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){weights cannot be all zero}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){is_log}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){x}<LSEP>[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){predictor variable `x` is not ...}<LSEP>[argument 1; litteral](str){and cannot be log-transformed}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){x}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){max_iter}<LEND>[call](){}<LSEP>[](symbol){ceiling}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){max_iter}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){max_iter}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){maximum number of iterations m...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){lower_bound}<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){is.numeric}<LSEP>[](symbol){lower_bound}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){lower_bound}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'lower_bound' must be a numeri...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){upper_bound}<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){is.numeric}<LSEP>[](symbol){upper_bound}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){upper_bound}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'upper_bound' must be a numeri...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){lower_bound}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){upper_bound}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){lower_bound}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){upper_bound}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'lower_bound' and 'upper_bound...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){upper_bound}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'lower_bound' cannot be larger...}<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){is.infinite}<LSEP>[](symbol){lower_bound}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){lower_bound}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'lower_bound' cannot be equal ...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){upper_bound}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){upper_bound}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'upper_bound' cannot be equal ...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){start}<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){is.numeric}<LSEP>[](symbol){start}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){start}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'start' must be a numeric vector}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.infinite}<LSEP>[](symbol){start}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){start}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){'start' must be finite}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){object}<LEND>[call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){mean_function}<LEND>[argument 1; call](){}<LSEP>[](symbol){logistic2_new}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){w}<LSEP>[](symbol){start}<LSEP>[](symbol){max_iter}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){upper_bound}<LEND>[argument 2; call](){}<LSEP>[](symbol){logistic4_new}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){w}<LSEP>[](symbol){start}<LSEP>[](symbol){max_iter}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){upper_bound}<LEND>[argument 3; call](){}<LSEP>[](symbol){logistic5_new}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){w}<LSEP>[](symbol){start}<LSEP>[](symbol){max_iter}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){upper_bound}<LEND>[argument 4; call](){}<LSEP>[](symbol){logistic6_new}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){w}<LSEP>[](symbol){start}<LSEP>[](symbol){max_iter}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){upper_bound}<LEND>[argument 5; call](){}<LSEP>[](symbol){gompertz_new}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){w}<LSEP>[](symbol){start}<LSEP>[](symbol){max_iter}<LSEP>[](symbol){lower_bound}<LSEP>[](symbol){upper_bound}<LEND>[statement 26; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){object}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){chosen 'mean_function' is wron...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){result}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){constrained}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){fit}<LSEP>[](symbol){object}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){fit_constrained}<LSEP>[](symbol){object}<LEND>[statement 28; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){mean_function}<LEND>[](symbol){mean_function}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){log_w}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){weights}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){v}<LEND>[call](){}<LSEP>[](symbol){variance_normal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){rss}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){df.residual}<LEND>[statement 31; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){n}<LEND>[statement 32; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){sigma}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LSEP>[](symbol){v}<LEND>[statement 33; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){loglik}<LEND>[call](){}<LSEP>[](symbol){loglik_normal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){rss}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){n}<LEND>[](symbol){log_w}<LEND>[statement 34; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){fisher.info}<LEND>[call](){}<LSEP>[](symbol){fisher_info}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){coefficients}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){sigma}<LEND>[statement 35; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){vcov}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){constrained}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){approx_vcov}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){fisher.info}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){fisher.info}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){idx}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){estimated}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){k}<LSEP>[](symbol){k}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vcov}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){idx}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){idx}<LEND>[call](){}<LSEP>[](symbol){approx_vcov}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){fisher.info}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){idx}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){idx}<LEND>[](symbol){vcov}<LEND>[statement 36; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){call}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 37; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){terms}<LEND>[](symbol){model_terms}<LEND>[statement 38; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){model}<LEND>[](symbol){model_frame}<LEND>[statement 39; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){na.action}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){model_frame}<LSEP>[argument 1; litteral](str){na.action}<LEND>[statement 40; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){is_log}<LEND>[](symbol){is_log}<LEND>[statement 41; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){drda}<LEND>[argument 1; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){result}<LEND>[](symbol){result}<LEND>[assign](){<-}<LSEP>[](symbol){anova.drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<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; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){named}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){the following arguments to 'an...}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){named}<LEND>[argument 1; litteral](str){, }<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dotargs}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dotargs}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){named}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){is_drda}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){dotargs}<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 5; assign](){<-}<LSEP>[](symbol){dotargs}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dotargs}<LSEP>[](symbol){is_drda}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dotargs}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){anova.drdalist}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){object}<LEND>[](symbol){dotargs}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){constrained}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){hypothesis testing is not avai...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){model}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){weights}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){idx}<LEND>[call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){w}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){idx}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){idx}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){idx}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LSEP>[](symbol){idx}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){log_n}<LEND>[call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){n}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){log_w}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){w}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){estimated}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){l}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](real){2.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; litteral](real){3.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){deviance_df}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){l}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){deviance_value}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){l}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){loglik}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){l}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){weighted_mean}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){w}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 22; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deviance_df}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 23; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deviance_value}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LSEP>[](symbol){weighted_mean}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 24; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deviance_df}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){df.residual}<LEND>[statement 25; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deviance_value}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){rss}<LEND>[statement 26; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fit}<LEND>[call](){}<LSEP>[](symbol){drda}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LEND>[](symbol){w}<LSEP>[argument 2; litteral](str){logistic5}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deviance_df}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fit}<LSEP>[](symbol){df.residual}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deviance_value}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fit}<LSEP>[](symbol){rss}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){loglik}<LEND>[call](){}<LSEP>[](symbol){loglik_normal}<LSEP>[](symbol){deviance_value}<LSEP>[](symbol){n}<LSEP>[](symbol){log_w}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[](symbol){deviance_df}<LEND>[statement 29; assign](){<-}<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){df}<LSEP>[](symbol){loglik}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){bic}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){log_n}<LSEP>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){loglik}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){lrt}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){loglik}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loglik}<LSEP>[](symbol){l}<LEND>[statement 32; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lrt}<LSEP>[](symbol){l}<LEND>[litteral](real){nan}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){table}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){deviance_df}<LSEP>[](symbol){deviance_value}<LSEP>[](symbol){df}<LSEP>[](symbol){aic}<LSEP>[](symbol){bic}<LSEP>[](symbol){lrt}<LEND>[statement 34; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){table}<LSEP>[](symbol){pvalue}<LEND>[call](){}<LSEP>[](symbol){pchisq}<LSEP>[](symbol){lrt}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){diff}<LSEP>[](symbol){deviance_df}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 35; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){table}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Constant model}<LSEP>[argument 1; litteral](str){Estimated model}<LEND>[statement 36; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){table}<LEND>[argument 1; litteral](real){3.000000}<LEND>[litteral](str){Full model (logistic5)}<LEND>[statement 37; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){table}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Resid. Df}<LSEP>[argument 1; litteral](str){Resid. Dev}<LSEP>[argument 2; litteral](str){Df}<LSEP>[argument 3; litteral](str){AIC}<LSEP>[argument 4; litteral](str){BIC}<LSEP>[argument 5; litteral](str){LRT}<LSEP>[argument 6; litteral](str){p-value}<LEND>[statement 38; assign](){<-}<LSEP>[](symbol){model}<LEND>[call](){}<LSEP>[](symbol){switch}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){mean_function}<LEND>[argument 1; litteral](str){2-parameter logistic}<LSEP>[argument 2; litteral](str){4-parameter logistic}<LSEP>[argument 3; litteral](str){5-parameter logistic}<LSEP>[argument 4; litteral](str){6-parameter logistic}<LEND>[statement 39; assign](){<-}<LSEP>[](symbol){title}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Analysis of Deviance Table\n\n...}<LSEP>[](symbol){model}<LSEP>[argument 2; litteral](str){\n}<LSEP>[argument 3; litteral](str){}<LEND>[statement 40; call](){}<LSEP>[](symbol){structure}<LSEP>[](symbol){table}<LSEP>[](symbol){title}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){anova}<LSEP>[argument 1; litteral](str){data.frame}<LEND>[assign](){<-}<LSEP>[](symbol){anova.drdalist}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n_models}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){object}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){n_models}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){anova.drda}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){object}<LSEP>[argument 1; litteral](integer){1}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){is_constrained}<LEND>[call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){object}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){constrained}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){is_constrained}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){hypothesis testing is not avai...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){n_residuals}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){object}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){residuals}<LEND>[argument 2; litteral](real){0.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){n_residuals}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){n_residuals}<LSEP>[argument 1; litteral](integer){1}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){models were not all fitted to ...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){Y}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){object}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){z}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){z}<LSEP>[](symbol){model}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){n_residuals}<LSEP>[argument 1; litteral](integer){1}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Y}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Y}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){y}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){models were not all fitted on ...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){X}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){object}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){z}<LEND>[body; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){z}<LSEP>[](symbol){model}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){n_residuals}<LSEP>[argument 1; litteral](integer){1}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){X}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){X}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){models were not all fitted on ...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){object}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){weights}<LEND>[argument 2; call](){}<LSEP>[](symbol){numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){n_residuals}<LSEP>[argument 1; litteral](integer){1}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){w}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){models were not all fitted wit...}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){idx}<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){is.na}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){w}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){idx}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LSEP>[](symbol){idx}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){idx}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){w}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){w}<LSEP>[](symbol){idx}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){n_obs}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){y}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){log_n}<LEND>[call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){n_obs}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){log_w}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){log}<LSEP>[](symbol){w}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){n_params}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){object}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){estimated}<LEND>[argument 2; litteral](real){0.000000}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){tmp_dev}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){object}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){rss}<LEND>[argument 2; litteral](real){0.000000}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){ord}<LEND>[call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){n_params}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){tmp_dev}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){object}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){object}<LSEP>[](symbol){ord}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){n_params}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){n_params}<LSEP>[](symbol){ord}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){tmp_dev}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tmp_dev}<LSEP>[](symbol){ord}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){tmp_df}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){object}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){df.residual}<LEND>[argument 2; litteral](real){0.000000}<LEND>[statement 27; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){n_params}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){df}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n_params}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n_params}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 29; assign](){<-}<LSEP>[](symbol){deviance_df}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){tmp_df}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){tmp_df}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){deviance_value}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){tmp_dev}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){tmp_dev}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){deviance_df}<LEND>[statement 32; assign](){<-}<LSEP>[](symbol){loglik}<LEND>[call](){}<LSEP>[](symbol){rep}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){l}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){weighted_mean}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){w}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){w}<LEND>[statement 34; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deviance_df}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_obs}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 35; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deviance_value}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){y}<LSEP>[](symbol){weighted_mean}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 36; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fit}<LEND>[call](){}<LSEP>[](symbol){drda}<LEND>[argument 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){y}<LSEP>[](symbol){x}<LEND>[](symbol){w}<LSEP>[argument 2; litteral](str){logistic5}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deviance_df}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fit}<LSEP>[](symbol){df.residual}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){deviance_value}<LSEP>[](symbol){l}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){fit}<LSEP>[](symbol){rss}<LEND>[statement 37; assign](){<-}<LSEP>[](symbol){loglik}<LEND>[call](){}<LSEP>[](symbol){loglik_normal}<LSEP>[](symbol){deviance_value}<LSEP>[](symbol){n_obs}<LSEP>[](symbol){log_w}<LEND>[statement 38; assign](){<-}<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){df}<LSEP>[](symbol){loglik}<LEND>[statement 39; assign](){<-}<LSEP>[](symbol){bic}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){log_n}<LSEP>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){loglik}<LEND>[statement 40; assign](){<-}<LSEP>[](symbol){lrt}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){loglik}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loglik}<LSEP>[](symbol){l}<LEND>[statement 41; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lrt}<LSEP>[](symbol){l}<LEND>[litteral](real){nan}<LEND>[statement 42; assign](){<-}<LSEP>[](symbol){table}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){deviance_df}<LSEP>[](symbol){deviance_value}<LSEP>[](symbol){df}<LSEP>[](symbol){aic}<LSEP>[](symbol){bic}<LSEP>[](symbol){lrt}<LEND>[statement 43; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){table}<LSEP>[](symbol){pvalue}<LEND>[call](){}<LSEP>[](symbol){pchisq}<LSEP>[](symbol){lrt}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){diff}<LSEP>[](symbol){deviance_df}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 44; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){table}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Resid. Df}<LSEP>[argument 1; litteral](str){Resid. Dev}<LSEP>[argument 2; litteral](str){Df}<LSEP>[argument 3; litteral](str){AIC}<LSEP>[argument 4; litteral](str){BIC}<LSEP>[argument 5; litteral](str){LRT}<LSEP>[argument 6; litteral](str){p-value}<LEND>[statement 45; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){table}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Model}<LEND>[argument 1; call](){}<LSEP>[](symbol){seq_len}<LSEP>[](symbol){l}<LEND>[statement 46; assign](){<-}<LSEP>[](symbol){title}<LSEP>[litteral](str){Analysis of Deviance Table\n}<LEND>[statement 47; assign](){<-}<LSEP>[](symbol){str}<LEND>[call](){}<LSEP>[](symbol){vapply}<LSEP>[](symbol){object}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){z}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){z}<LSEP>[](symbol){mean_function}<LEND>[argument 2; litteral](str){string}<LEND>[statement 48; assign](){<-}<LSEP>[](symbol){str}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Model }<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){n_models}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){: }<LSEP>[](symbol){str}<LSEP>[argument 4; litteral](str){}<LEND>[statement 49; assign](){<-}<LSEP>[](symbol){topnote}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){5.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){str}<LSEP>[](symbol){n_models}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){str}<LSEP>[](symbol){n_models}<LEND>[argument 1; litteral](str){(Full)}<LEND>[statement 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Model 1: Constant}<LSEP>[](symbol){str}<LSEP>[argument 2; litteral](str){\n}<LEND>[argument 1; litteral](str){\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Model 1: Constant}<LSEP>[](symbol){str}<LEND>[argument 2; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Model }<LSEP>[](symbol){l}<LSEP>[argument 2; litteral](str){: logistic5 (Full)\n}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; litteral](str){\n}<LEND>[statement 50; assign](){<-}<LSEP>[](symbol){comment}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Model}<LEND>[argument 1; call](){}<LSEP>[](symbol){which.min}<LSEP>[](symbol){aic}<LEND>[argument 2; litteral](str){is the best model according to...}<LEND>[statement 51; call](){}<LSEP>[](symbol){structure}<LSEP>[](symbol){table}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){title}<LSEP>[](symbol){topnote}<LSEP>[](symbol){comment}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){anova}<LSEP>[argument 1; litteral](str){data.frame}<LEND>[assign](){<-}<LSEP>[](symbol){deviance.drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){rss}<LEND>[assign](){<-}<LSEP>[](symbol){logLik.drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){loglik}<LEND>[assign](){<-}<LSEP>[](symbol){predict.drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<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){missing}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){fitted.values}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){\|\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){variable `x` is not a numeric ...}<LEND>[statement 2; call](){}<LSEP>[](symbol){fn}<LSEP>[](symbol){object}<LSEP>[](symbol){x}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){coefficients}<LEND>[assign](){<-}<LSEP>[](symbol){print.drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){digits}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nCall:\n}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){call}<LEND>[argument 1; litteral](str){\n}<LSEP>[argument 2; litteral](str){\n}<LEND>[argument 2; litteral](str){\n\n}<LSEP>[argument 3; litteral](str){}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){coefficients}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Coefficients:\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){print.default}<LEND>[argument 0; call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){coefficients}<LEND>[](symbol){digits}<LEND>[argument 1; litteral](integer){2}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){No coefficients\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}<LEND>[assign](){<-}<LSEP>[](symbol){print.summary.drda}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){digits}<LSEP>[](symbol){symbolic.cor}<LSEP>[](symbol){signif.stars}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nCall: }<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){call}<LEND>[argument 1; litteral](str){\n}<LSEP>[argument 2; litteral](str){\n}<LEND>[argument 2; litteral](str){\n}<LSEP>[argument 3; litteral](str){}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nPearson Residuals:\n}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){pearson_resid}<LEND>[call](){}<LSEP>[](symbol){setNames}<LEND>[argument 0; call](){}<LSEP>[](symbol){quantile}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){pearson_resid}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Min}<LSEP>[argument 1; litteral](str){1Q}<LSEP>[argument 2; litteral](str){Median}<LSEP>[argument 3; litteral](str){3Q}<LSEP>[argument 4; litteral](str){Max}<LEND>[statement 3; call](){}<LSEP>[](symbol){print.default}<LEND>[argument 0; call](){}<LSEP>[](symbol){zapsmall}<LSEP>[](symbol){pearson_resid}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){digits}<LSEP>[argument 1; litteral](integer){1}<LEND>[](symbol){digits}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](integer){2}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nParameters:\n}<LEND>[statement 5; call](){}<LSEP>[](symbol){printCoefmat}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){param}<LEND>[](symbol){digits}<LEND>[argument 2; call](){}<LSEP>[](symbol){numeric}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 3; litteral](logical){FALSE}<LSEP>[argument 4; litteral](logical){FALSE}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nResidual standard error on}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){df.residual}<LEND>[argument 2; litteral](str){degrees of freedom\n}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){msg}<LEND>[call](){}<LSEP>[](symbol){naprint}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){na.action}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){nzchar}<LSEP>[](symbol){msg}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ (}<LSEP>[](symbol){msg}<LSEP>[argument 2; litteral](str){)\n}<LSEP>[argument 3; litteral](str){}<LEND>[statement 9; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nLog-likelihood:}<LEND>[argument 1; call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){loglik}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](integer){4}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){digits}<LSEP>[argument 1; litteral](integer){1}<LEND>[statement 10; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nAIC:}<LEND>[argument 1; call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){aic}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](integer){4}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){digits}<LSEP>[argument 1; litteral](integer){1}<LEND>[statement 11; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nBIC:}<LEND>[argument 1; call](){}<LSEP>[](symbol){format}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){bic}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[argument 0; litteral](integer){4}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){digits}<LSEP>[argument 1; litteral](integer){1}<LEND>[statement 12; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){converged}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nOptimization algorithm conve...}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){iterations}<LEND>[argument 2; litteral](str){iterations\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\nOptimization algorithm DID N...}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<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; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){weights}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl2phylip}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){outfile}<LSEP>[](symbol){outpath}<LSEP>[](symbol){bstrap}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){outfilespec}<LEND>[call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){outpath}<LSEP>[](symbol){outfile}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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}
[](){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}
[](){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}
[](){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; litteral](real){4.000000}<LEND>[](symbol){v}<LEND>[](symbol){stats}<LEND>[assign](){<-}<LSEP>[](symbol){variance_normal}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){rss}<LSEP>[](symbol){df}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){rss}<LSEP>[](symbol){df}<LEND>[assign](){<-}<LSEP>[](symbol){loglik_normal}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){deviance}<LSEP>[](symbol){n}<LSEP>[](symbol){log_w}<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){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){pi}<LEND>[](symbol){deviance}<LEND>[](symbol){n}<LEND>[](symbol){log_w}<LEND>[argument 1; litteral](real){2.000000}<LEND>[assign](){<-}<LSEP>[](symbol){approx_vcov}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){fim}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){tryCatch}<LEND>[argument 0; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){chol2inv}<LEND>[argument 0; call](){}<LSEP>[](symbol){chol}<LSEP>[](symbol){fim}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){e}<LEND>[body; block](){}<LSEP>[statement 0; litteral](NULL){NULL}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){vcov}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){tryCatch}<LEND>[argument 0; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){chol2inv}<LEND>[argument 0; call](){}<LSEP>[](symbol){chol}<LSEP>[](symbol){fim}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){e}<LEND>[body; block](){}<LSEP>[statement 0; litteral](NULL){NULL}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){vcov}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){vcov}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){fim}<LEND>[argument 2; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){fim}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){lab}<LEND>[call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){fim}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){vcov}<LEND>[](symbol){lab}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){vcov}<LEND>[](symbol){lab}<LEND>[](symbol){vcov}<LEND>[assign](){<-}<LSEP>[](symbol){fit_nlminb}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){start}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){control}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](integer){1000}<LSEP>[argument 1; litteral](integer){1000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){f}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){constrained}<LEND>[true branch; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){nlminb}<LSEP>[](symbol){x}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){control}<LEND>[statement 1; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){mle_asy}<LSEP>[](symbol){object}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){y}<LSEP>[](symbol){par}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){y}<LSEP>[](symbol){iterations}<LEND>[false branch; block](){}<LSEP>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){nlminb}<LSEP>[](symbol){x}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){control}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[statement 1; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){y}<LSEP>[](symbol){par}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){y}<LSEP>[](symbol){iterations}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){best_par}<LEND>[call](){}<LSEP>[](symbol){rep}<LSEP>[argument 0; litteral](real){nan}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){start}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){best_rss}<LSEP>[litteral](real){inf}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){best_iter}<LSEP>[litteral](integer){1000}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){seq_len}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){start}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){tryCatch}<LEND>[argument 0; call](){}<LSEP>[](symbol){suppressWarnings}<LEND>[argument 0; call](){}<LSEP>[](symbol){f}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){start}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){e}<LEND>[body; litteral](NULL){NULL}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){tmp}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){current_rss}<LEND>[call](){}<LSEP>[](symbol){rss_fn}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){par}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){current_rss}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){current_rss}<LSEP>[](symbol){best_rss}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){best_par}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){par}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){best_rss}<LSEP>[](symbol){current_rss}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){best_iter}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){niter}<LEND>[statement 6; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){best_par}<LSEP>[](symbol){best_rss}<LSEP>[](symbol){best_iter}<LEND>[assign](){<-}<LSEP>[](symbol){find_optimum}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){start}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){start}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){start}<LEND>[argument 1; litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){init}<LSEP>[](symbol){object}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rss_fn}<LEND>[call](){}<LSEP>[](symbol){rss}<LSEP>[](symbol){object}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rss_gh}<LEND>[call](){}<LSEP>[](symbol){rss_gradient_hessian}<LSEP>[](symbol){object}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){update_fn}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){theta}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){mle_asy}<LSEP>[](symbol){object}<LSEP>[](symbol){theta}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){solution}<LEND>[call](){}<LSEP>[](symbol){ntrm}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){rss_gh}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){start}<LSEP>[](symbol){theta}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){max_iter}<LEND>[](symbol){update_fn}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){iterations}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){iterations}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){start}<LSEP>[](symbol){niter}<LEND>[](symbol){solution}<LEND>[assign](){<-}<LSEP>[](symbol){find_optimum_constrained}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){object}<LSEP>[](symbol){constraint}<LSEP>[](symbol){known_param}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){start}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){start}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){known_param}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){start}<LEND>[](symbol){known_param}<LEND>[argument 1; litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){init}<LSEP>[](symbol){object}<LEND>[statement 1; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){ifelse}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){known_param}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){theta}<LEND>[](symbol){known_param}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tmp}<LSEP>[](symbol){niter}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){solution}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){constraint}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){idx}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){constraint}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rss_fn}<LEND>[call](){}<LSEP>[](symbol){rss_fixed}<LSEP>[](symbol){object}<LSEP>[](symbol){known_param}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){rss_gh}<LEND>[call](){}<LSEP>[](symbol){rss_gradient_hessian_fixed}<LSEP>[](symbol){object}<LSEP>[](symbol){known_param}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){constraint}<LSEP>[](symbol){idx}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){ntrm}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){rss_gh}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){start}<LSEP>[](symbol){theta}<LEND>[](symbol){idx}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){max_iter}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){ntrm_constrained}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){rss_gh}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){start}<LSEP>[](symbol){theta}<LEND>[](symbol){idx}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){max_iter}<LEND>[argument 4; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[](symbol){idx}<LEND>[argument 5; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[](symbol){idx}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rss_fn}<LEND>[call](){}<LSEP>[](symbol){rss}<LSEP>[](symbol){object}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rss_gh}<LEND>[call](){}<LSEP>[](symbol){rss_gradient_hessian}<LSEP>[](symbol){object}<LEND>[statement 2; call](){}<LSEP>[](symbol){ntrm_constrained}<LSEP>[](symbol){rss_fn}<LSEP>[](symbol){rss_gh}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){start}<LSEP>[](symbol){theta}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){max_iter}<LEND>[argument 4; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){lower_bound}<LEND>[argument 5; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){object}<LSEP>[](symbol){upper_bound}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){iterations}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){solution}<LSEP>[](symbol){iterations}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){start}<LSEP>[](symbol){niter}<LEND>[](symbol){solution}
[](){expression}<LSEP>[litteral](NULL){NULL}
[](){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}
[](){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}
[](){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; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){folder}<LEND>[argument 2; litteral](str){ folder(s)...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){base}<LSEP>[](symbol){dwdbase}<LEND>[true branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){folder}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){base is not the rdwd default. ...}<LSEP>[argument 1; litteral](str){ to use folder="" instead of "}<LSEP>[](symbol){folder}<LSEP>[argument 3; litteral](str){".}<LEND>[statement 5; control flow](){if}<LSEP>[](symbol){progbar}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){lapply}<LEND>[call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){pbapply}<LSEP>[](symbol){pblapply}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){curl_handle}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RCurl}<LSEP>[](symbol){getCurlHandle}<LEND>[argument 0; litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){base}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){/+$}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){base}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){folder}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){^/+}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){folder}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){df_ff}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){folder}<LSEP>[argument 1; litteral](logical){FALSE}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 10; control flow](){if}<LSEP>[](symbol){is.file.if.has.dot}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df_ff}<LSEP>[](symbol){isfile}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){.}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df_ff}<LSEP>[](symbol){path}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[litteral](logical){TRUE}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){getURL_ffe}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){ff_row}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){stoppp_ffe}<LEND>[true branch; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){ff_row}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){try}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){RCurl}<LSEP>[](symbol){getURL}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){base}<LSEP>[argument 1; litteral](str){/}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ff_row}<LSEP>[](symbol){path}<LEND>[argument 3; litteral](str){/}<LEND>[](symbol){verbose}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[](symbol){curl_handle}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](str){try-error}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){Error in function (type, msg, ...}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){p}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){removeSpace}<LEND>[argument 0; call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){\n}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){p}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){Could not resolve host}<LSEP>[](symbol){p}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](str){\nThis may mean you are not co...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){Server denied you to change to...}<LSEP>[](symbol){p}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](str){\nThis could mean the path is ...}<LSEP>[argument 2; litteral](str){ or that it doesn't exist at b...}<LSEP>[](symbol){base}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){msg}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){traceCall}<LSEP>[argument 0; litteral](real){3.000000}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){: }<LEND>[argument 1; litteral](str){RCurl::getURL failed for '}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ff_row}<LSEP>[](symbol){path}<LEND>[argument 3; litteral](str){/' with error:\n - }<LSEP>[](symbol){p}<LEND>[statement 5; call](){}<LSEP>[](symbol){warning}<LSEP>[](symbol){msg}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 6; call](){}<LSEP>[](symbol){assign}<LSEP>[argument 0; litteral](str){stoppp_ffe}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 7; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){ff_row}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](str){[\n\r]}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){ilf}<LEND>[call](){}<LSEP>[](symbol){grep}<LSEP>[argument 0; litteral](str){latest-dwd---bin}<LSEP>[](symbol){p}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ilf}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; control flow](){if}<LSEP>[](symbol){exclude.latest.bin}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ilf}<LEND>[false branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){ilf}<LEND>[call](){}<LSEP>[](symbol){sub}<LSEP>[argument 0; litteral](str){ -> .*}<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){p}<LSEP>[](symbol){ilf}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){isdir}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){substr}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](str){d}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){pnames}<LEND>[call](){}<LSEP>[](symbol){read.table}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){pnames}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pnames}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){pnames}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){output}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ff_row}<LSEP>[](symbol){path}<LEND>[argument 1; litteral](str){/}<LSEP>[](symbol){pnames}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){isdir}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){sleep}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){Sys.sleep}<LEND>[argument 0; call](){}<LSEP>[](symbol){runif}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[](symbol){sleep}<LEND>[statement 12; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){output}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){stoppp_ffe}<LSEP>[litteral](logical){FALSE}<LEND>[statement 13; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df_ff}<LSEP>[](symbol){isfile}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){df_ff}<LEND>[call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){df_ff}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){df_ff1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df_ff}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df_ff}<LSEP>[](symbol){isfile}<LEND>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){df_ff2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df_ff}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df_ff}<LSEP>[](symbol){isfile}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){df_ff3}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){df_ff2}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LEND>[body; call](){}<LSEP>[](symbol){getURL_ffe}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df_ff2}<LSEP>[](symbol){r}<LSEP>[](symbol){}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){df_ff}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[](symbol){rbind}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){df_ff1}<LEND>[](symbol){df_ff3}<LEND>[statement 5; control flow](){if}<LSEP>[](symbol){stoppp_ffe}<LSEP>[true branch; control flow](){break}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){anyDuplicated}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df_ff}<LSEP>[](symbol){path}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Duplicate paths:}<LEND>[argument 1; call](){}<LSEP>[](symbol){truncMessage}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df_ff}<LSEP>[](symbol){path}<LEND>[argument 1; call](){}<LSEP>[](symbol){duplicated}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df_ff}<LSEP>[](symbol){path}<LEND>[argument 1; litteral](str){}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){finalpaths}<LEND>[call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df_ff}<LSEP>[](symbol){path}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){owd}<LEND>[call](){}<LSEP>[](symbol){dirDWD}<LSEP>[](symbol){dir}<LSEP>[](symbol){quiet}<LEND>[statement 17; call](){}<LSEP>[](symbol){on.exit}<LEND>[argument 0; call](){}<LSEP>[](symbol){setwd}<LSEP>[](symbol){owd}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){outfile}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; 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}
[](){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; assign](){<-}<LSEP>[](symbol){numrows}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){df0}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){numcols}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){df0}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 11; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Input data should be a csv fil...}<LEND>[statement 12; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){numcols}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){loci, confirming first 5:}<LEND>[argument 3; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df0}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[argument 4; litteral](str){\n}<LEND>[statement 13; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){numrows}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){individuals, confirming first 5:}<LEND>[argument 3; call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df0}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[argument 2; litteral](real){1.000000}<LEND>[argument 4; litteral](str){\n}<LEND>[statement 14; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ If these are reversed, re-...}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df0}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){numrows}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){numcols}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){loci}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df0}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){numcols}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){loci}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){loci}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){individuals}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df0}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){numrows}<LEND>[argument 2; litteral](real){1.000000}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){individuals}<LEND>[call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){individuals}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){individuals}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){individuals}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: Individual labels...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){unique}<LSEP>[](symbol){loci}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){loci}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: AlleleID not uniq...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){test}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](str){}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){test}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){NA}<LSEP>[argument 1; litteral](str){9}<LSEP>[](symbol){test}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){test}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){ }<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){test}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){test}<LEND>[argument 1; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){data}<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){Character data detected, assum...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){s1}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){s1}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){/}<LSEP>[argument 1; litteral](str){ }<LSEP>[](symbol){s1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){s1}<LEND>[call](){}<LSEP>[](symbol){toupper}<LSEP>[](symbol){s1}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){s2}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){s1}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){s2}<LEND>[statement 6; 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){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](str){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](str){C}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](str){G}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](str){T}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](str){-}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: Genotypes must be...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](real){2.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){v1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){v1}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){v1}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){v1}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){/}<LSEP>[argument 1; litteral](str){ }<LSEP>[](symbol){v1}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){v1}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){- }<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){v1}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){v1}<LEND>[call](){}<LSEP>[](symbol){toupper}<LSEP>[](symbol){v1}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){v1}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){v1}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){v1}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: Loci are not bial...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<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; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Data confirmed as biallelic\n}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){homRef}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){/}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){homAlt}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){/}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){het1}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](str){/}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){het2}<LEND>[call](){}<LSEP>[](symbol){paste0}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](str){/}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){missing}<LSEP>[litteral](str){-/-}<LEND>[statement 14; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){data}<LEND>[argument 1; litteral](real){2.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){toupper}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){homRef}<LSEP>[argument 1; litteral](str){0}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){homAlt}<LSEP>[argument 1; litteral](str){2}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){het1}<LSEP>[argument 1; litteral](str){1}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){het2}<LSEP>[argument 1; litteral](str){1}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[](symbol){missing}<LSEP>[argument 1; litteral](logical){NA}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 15; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ SNP coding converted to 0,1,...}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){as.numeric}<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){Numeric data detected, assume ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){as.numeric}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){s1}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){s2}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LSEP>[](symbol){s1}<LSEP>[argument 1; litteral](str){ }<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){s2}<LEND>[statement 5; 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){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](str){0}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](str){1}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](str){2}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](str){NA}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: Genotypes must be...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){as.genlight}<LSEP>[](symbol){data}<LEND>[statement 27; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){gl}<LEND>[](symbol){loci}<LEND>[statement 28; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){gl}<LEND>[](symbol){individuals}<LEND>[statement 29; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](str){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){gl}<LEND>[statement 30; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){gl}<LEND>[argument 1; call](){}<LSEP>[](symbol){locNames}<LSEP>[](symbol){gl}<LEND>[statement 31; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){ind.metrics}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; assign](){<-}<LSEP>[](symbol){id}<LEND>[call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){gl}<LEND>[argument 1; call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](str){A}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){gl}<LEND>[statement 32; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){loc.metafile}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){loc.metrics}<LEND>[call](){}<LSEP>[](symbol){read.csv}<LSEP>[](symbol){loc.metafile}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){AlleleID}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){loc.metrics}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: mandatory AlleleI...}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){gl}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){loc.metrics}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){AlleleID}<LEND>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Fatal Error: AlleleID in the l...}<LSEP>[argument 1; litteral](str){AlleleID in the input data fil...}<LEND>[statement 1; call](){}<LSEP>[](symbol){stop}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<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}
[](){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){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[statement 8; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){parsed}
[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){.noGenerics}<LSEP>[litteral](logical){TRUE}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl2demerelate}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){gl}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){x}<LSEP>[](symbol){gl}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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}
[](){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}
[](){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; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){storage.mode}<LSEP>[](symbol){step.matrix}<LEND>[litteral](str){double}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){.Call}<LSEP>[](symbol){C_computeCM_Call}<LSEP>[](symbol){wm}<LSEP>[](symbol){lm}<LSEP>[](symbol){cm}<LSEP>[](symbol){step.matrix}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Native dtw implementation not ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){dir}<LSEP>[](symbol){step.matrix}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){npats}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dir}<LSEP>[argument 1; litteral](str){npat}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){m}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){window.function}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LSEP>[](symbol){n}<LSEP>[](symbol){m}<LSEP>[](symbol){...}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){next}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cm}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){next}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){clist}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){numeric}<LSEP>[](symbol){npats}<LEND>[argument 1; litteral](logical){NA}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){s}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; 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; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){out}
[](){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}
[](){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; litteral](str){ Warning: Method not in the li...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){method}<LSEP>[litteral](str){simple}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){nI}<LEND>[call](){}<LSEP>[](symbol){nInd}<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; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating the distance mat...}<LSEP>[](symbol){method}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 13; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){nI}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){nI}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){row1}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){row2}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mat}<LSEP>[](symbol){j}<LSEP>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){a11}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){row1}<LSEP>[](symbol){row2}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){a10}<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){row1}<LSEP>[](symbol){row2}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){row1}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){a01}<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){row1}<LSEP>[](symbol){row2}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){row2}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){a00}<LEND>[call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){row1}<LSEP>[](symbol){row2}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){a11}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){a01}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){a10}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){d}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){a00}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){simple}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[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){a}<LSEP>[](symbol){d}<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){a}<LSEP>[](symbol){b}<LEND>[](symbol){c}<LEND>[](symbol){d}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){jaccard}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){a}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){a}<LSEP>[](symbol){b}<LEND>[](symbol){c}<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){method}<LSEP>[argument 1; litteral](str){dice}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){sorenson}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){czekanowski}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){a}<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>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){a}<LEND>[](symbol){b}<LEND>[](symbol){c}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[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){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){a}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){b}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){a}<LSEP>[](symbol){b}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){a}<LSEP>[](symbol){c}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){d}<LSEP>[](symbol){b}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){d}<LSEP>[](symbol){c}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dd}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LEND>[litteral](real){0.000000}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Converting to a distance obj...}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){dd}<LEND>[call](){}<LSEP>[](symbol){as.dist}<LSEP>[](symbol){dd}<LEND>[statement 16; 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 17; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){dd}
[](){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; 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>[](symbol){k}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){listdf}<LSEP>[](symbol){k}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){listdf}<LSEP>[](symbol){k}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){foldh}<LEND>[call](){}<LSEP>[](symbol){folderh}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){listdf}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){classes}<LSEP>[argument 1; 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}
[](){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}
[](){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}
[](){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}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.plot.network}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){D}<LSEP>[](symbol){x}<LSEP>[](symbol){method}<LSEP>[](symbol){node.size}<LSEP>[](symbol){node.label}<LSEP>[](symbol){node.label.size}<LSEP>[](symbol){node.label.color}<LSEP>[](symbol){alpha}<LSEP>[](symbol){title}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pkg}<LSEP>[litteral](str){igraph}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){requireNamespace}<LSEP>[](symbol){pkg}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Package}<LSEP>[](symbol){pkg}<LSEP>[argument 2; litteral](str){ needed for this function to w...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; 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; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; 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 6; 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 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){D}<LSEP>[argument 1; litteral](str){dist}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){D}<LSEP>[argument 1; litteral](str){matrix}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: distance matrix r...}<LEND>[statement 8; 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){!=}<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: if specified, gen...}<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){Note: genlight object not spec...}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){\|\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){\|\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){fr}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){kk}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){drl}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Layout method must be...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){method}<LSEP>[litteral](str){fr}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){D}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){len}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){links}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<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){len}<LSEP>[](symbol){len}<LEND>[](symbol){len}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){count}<LSEP>[litteral](real){1.000000}<LEND>[statement 14; control flow](){for}<LSEP>[](symbol){i}<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){len}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){len}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){links}<LSEP>[](symbol){count}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){m}<LEND>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){links}<LSEP>[](symbol){count}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){m}<LEND>[](symbol){j}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){links}<LSEP>[](symbol){count}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[statement 3; 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}
[](){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}
[](){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}
[](){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; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){2.000000}<LSEP>[](symbol){is.numeric}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The variables must be numeric!}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){There are NAs in the folder}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){windowh}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.numeric}<LSEP>[](symbol){windowh}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){windowh}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){windowh must be either a numer...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){windowh}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){windowh must be strictly posit...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){windowh}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){windowh}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The elements of the windowh li...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){windowh}<LEND>[](symbol){levgroup}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The names of the windowh list ...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){p}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){windowh}<LSEP>[](symbol){det}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){All elements of windowh must b...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){windowh}<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){All elements of windowh must b...}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){gaussiand}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){kern}<LSEP>[litteral](str){gauss}<LEND>[false branch; assign](){=}<LSEP>[](symbol){kern}<LSEP>[litteral](str){}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){group}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){There should be more than one ...}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){nb.groups}<LSEP>[](symbol){nb.values}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nb.values}<LSEP>[](symbol){nb.groups}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){nb.groups}<LSEP>[](symbol){nb.factors}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nb.factors}<LSEP>[](symbol){nb.groups}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){moyL}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[](symbol){group}<LSEP>[](symbol){colMeans}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){moyL0}<LSEP>[](symbol){moyL}<LEND>[statement 18; control flow](){if}<LSEP>[](symbol){data.centered}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){moyL}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){numeric}<LSEP>[](symbol){p}<LEND>[statement 1; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){scale}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){F}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){varL}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[](symbol){group}<LSEP>[](symbol){var}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){varL0}<LSEP>[](symbol){varL}<LEND>[statement 21; assign](){=}<LSEP>[](symbol){corL}<LSEP>[](symbol){varL}<LEND>[statement 22; 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; assign](){<-}<LSEP>[](symbol){corL}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[](symbol){group}<LSEP>[](symbol){cor}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){corL}<LSEP>[](symbol){i}<LEND>[litteral](real){1.000000}<LEND>[statement 23; control flow](){if}<LSEP>[](symbol){data.scaled}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){varL}<LSEP>[](symbol){corL}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){scale}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 24; control flow](){if}<LSEP>[](symbol){common.variance}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){var}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){skewnessL}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[](symbol){group}<LSEP>[](symbol){apply}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[](symbol){skewness}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){kurtosisL}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[](symbol){group}<LSEP>[](symbol){apply}<LSEP>[argument 3; litteral](real){2.000000}<LSEP>[](symbol){kurtosis}<LEND>[statement 27; assign](){=}<LSEP>[](symbol){choix}<LEND>[call](){}<LSEP>[](symbol){character}<LSEP>[argument 0; litteral](real){4.000000}<LEND>[statement 28; 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; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[litteral](str){m}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[litteral](str){u}<LEND>[statement 29; control flow](){if}<LSEP>[](symbol){gaussiand}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[litteral](str){g}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[litteral](str){n}<LEND>[statement 30; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){kern}<LSEP>[argument 1; litteral](str){gauss}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[litteral](str){g}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[litteral](str){.}<LEND>[statement 31; control flow](){if}<LSEP>[](symbol){gaussiand}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[litteral](str){.}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){windowh}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[litteral](str){a}<LEND>[false branch; block](){}<LSEP>[statement 0; 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){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){windowh}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[litteral](str){n}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[litteral](str){l}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){windowh}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[litteral](str){l}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[litteral](str){n}<LEND>[statement 32; assign](){=}<LSEP>[](symbol){choix}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){choix}<LSEP>[argument 1; litteral](str){}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){W}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){nb.groups}<LSEP>[](symbol){nb.groups}<LEND>[statement 34; call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){choix}<LEND>[argument 1; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Singular covariance matrix (gr...}<LEND>[argument 1; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){varL}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){)}<LEND>[argument 1; litteral](str){}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){l2dpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){moyL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){moyL}<LSEP>[](symbol){j}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){j}<LEND>[argument 2; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Singular covariance matrix (gr...}<LEND>[argument 1; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){varL}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](str){)}<LEND>[argument 1; litteral](str){}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){l2dpar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){moyL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){moyL}<LSEP>[](symbol){j}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){j}<LEND>[argument 3; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nbL}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){group}<LSEP>[](symbol){nrow}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){wL}<LEND>[call](){}<LSEP>[](symbol){bandwidth.parameter}<LSEP>[](symbol){p}<LSEP>[](symbol){nbL}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){varL}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){wL}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The matrices are not invertible}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xj}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){j}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){l2d}<LSEP>[](symbol){xi}<LSEP>[](symbol){xj}<LSEP>[argument 2; litteral](str){kern}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[argument 4; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){j}<LEND>[argument 4; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nbL}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[](symbol){group}<LSEP>[](symbol){NROW}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){wL}<LEND>[call](){}<LSEP>[](symbol){bandwidth.parameter}<LSEP>[](symbol){p}<LSEP>[](symbol){nbL}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){varL}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){wL}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){One variance or more is equal ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xj}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){j}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){l2d}<LSEP>[](symbol){xi}<LSEP>[](symbol){xj}<LSEP>[argument 2; litteral](str){kern}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[argument 4; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){j}<LEND>[argument 5; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nbL}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){group}<LSEP>[](symbol){nrow}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){varL}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){windowh}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The matrices are not invertible}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xj}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){j}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){l2d}<LSEP>[](symbol){xi}<LSEP>[](symbol){xj}<LSEP>[argument 2; litteral](str){kern}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[argument 4; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){j}<LEND>[argument 6; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nbL}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[](symbol){group}<LSEP>[](symbol){NROW}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){varL}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){windowh}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){One variance or more is equal ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xj}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){j}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){l2d}<LSEP>[](symbol){xi}<LSEP>[](symbol){xj}<LSEP>[argument 2; litteral](str){kern}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){i}<LEND>[argument 4; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){varLwL}<LSEP>[](symbol){j}<LEND>[argument 7; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nbL}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[](symbol){group}<LSEP>[](symbol){nrow}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){gi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[](symbol){gi}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){gj}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){j}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xj}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[](symbol){gj}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){l2d}<LSEP>[](symbol){xi}<LSEP>[](symbol){xj}<LSEP>[argument 2; litteral](str){kern}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){windowh}<LSEP>[](symbol){gi}<LEND>[argument 4; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){windowh}<LSEP>[](symbol){gj}<LEND>[argument 8; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){nbL}<LEND>[call](){}<LSEP>[](symbol){by}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[](symbol){group}<LSEP>[](symbol){NROW}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){gi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xi}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[](symbol){gi}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){gj}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){j}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){xj}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LEND>[](symbol){gj}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){l2d}<LSEP>[](symbol){xi}<LSEP>[](symbol){xj}<LSEP>[argument 2; litteral](str){kern}<LEND>[argument 3; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){windowh}<LSEP>[](symbol){gi}<LEND>[argument 4; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){windowh}<LSEP>[](symbol){gj}<LEND>[statement 35; control flow](){for}<LSEP>[](symbol){i}<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){nb.groups}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[statement 36; assign](){<-}<LSEP>[](symbol){norme}<LEND>[call](){}<LSEP>[](symbol){vector}<LSEP>[argument 0; litteral](str){numeric}<LSEP>[](symbol){nb.groups}<LEND>[statement 37; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){norme}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LEND>[statement 38; control flow](){if}<LSEP>[](symbol){normed}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<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 1; control flow](){for}<LSEP>[](symbol){i}<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){nb.groups}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[statement 39; control flow](){if}<LSEP>[](symbol){centered}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){moyW}<LEND>[call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){W}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){moycolW}<LEND>[call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){W}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){i}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){moycolW}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){moycolW}<LSEP>[](symbol){j}<LEND>[](symbol){moyW}<LEND>[statement 3; control flow](){for}<LSEP>[](symbol){i}<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){nb.groups}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){j}<LSEP>[](symbol){i}<LEND>[statement 40; assign](){<-}<LSEP>[](symbol){ep}<LEND>[call](){}<LSEP>[](symbol){svd}<LSEP>[](symbol){W}<LEND>[statement 41; assign](){<-}<LSEP>[](symbol){epaff}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ep}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.values}<LEND>[statement 42; assign](){<-}<LSEP>[](symbol){valpsqrt}<LEND>[call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ep}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.factors}<LEND>[statement 43; assign](){<-}<LSEP>[](symbol){coor}<LEND>[call](){}<LSEP>[](symbol){%%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ep}<LSEP>[](symbol){u}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.factors}<LEND>[argument 1; call](){}<LSEP>[](symbol){diag}<LEND>[argument 0; call](){}<LSEP>[](symbol){sign}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ep}<LSEP>[](symbol){u}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.factors}<LEND>[](symbol){valpsqrt}<LEND>[statement 44; assign](){<-}<LSEP>[](symbol){qual}<LSEP>[](symbol){coor}<LEND>[statement 45; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.groups}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){qual}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){1000.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){coor}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){W}<LSEP>[](symbol){i}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){10.000000}<LEND>[statement 46; assign](){<-}<LSEP>[](symbol){cont}<LSEP>[](symbol){coor}<LEND>[statement 47; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.factors}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cont}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){1000.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ep}<LSEP>[](symbol){u}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nb.factors}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){10.000000}<LEND>[statement 48; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){moyL}<LEND>[](symbol){dimnames}<LEND>[](symbol){last.column.name}<LEND>[statement 49; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){varL}<LEND>[](symbol){dimnames}<LEND>[](symbol){last.column.name}<LEND>[statement 50; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){corL}<LEND>[](symbol){dimnames}<LEND>[](symbol){last.column.name}<LEND>[statement 51; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){skewnessL}<LEND>[](symbol){dimnames}<LEND>[](symbol){last.column.name}<LEND>[statement 52; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){attributes}<LSEP>[](symbol){kurtosisL}<LEND>[](symbol){dimnames}<LEND>[](symbol){last.column.name}<LEND>[statement 53; assign](){<-}<LSEP>[](symbol){results}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[](symbol){last.column.name}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[argument 3; call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){epaff}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){1000.000000}<LSEP>[](symbol){epaff}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ep}<LSEP>[](symbol){d}<LEND>[argument 1; litteral](real){10.000000}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[argument 4; call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){cont}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 5; call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){qual}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 6; call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){coor}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 7; call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){levgroup}<LSEP>[](symbol){norme}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[](symbol){moyL}<LSEP>[](symbol){varL}<LSEP>[](symbol){corL}<LSEP>[](symbol){skewnessL}<LSEP>[](symbol){kurtosisL}<LEND>[statement 54; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){results}<LSEP>[](symbol){contributions}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){last.column.name}<LEND>[statement 55; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){results}<LSEP>[](symbol){qualities}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){last.column.name}<LEND>[statement 56; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){results}<LSEP>[](symbol){scores}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){last.column.name}<LEND>[statement 57; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){results}<LSEP>[](symbol){norm}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){last.column.name}<LEND>[statement 58; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){results}<LEND>[litteral](str){fpcad}<LEND>[statement 59; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){filename}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){save}<LSEP>[](symbol){results}<LSEP>[](symbol){filename}<LEND>[statement 60; control flow](){if}<LSEP>[](symbol){plot.eigen}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){inertia}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){results}<LSEP>[](symbol){inertia}<LEND>[](symbol){inertia}<LEND>[statement 1; call](){}<LSEP>[](symbol){barplot}<LSEP>[](symbol){inertia}<LSEP>[argument 1; litteral](str){Inertia}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){inertia}<LEND>[argument 3; litteral](real){1.000000}<LEND>[statement 61; control flow](){if}<LSEP>[](symbol){plot.score}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){results}<LSEP>[](symbol){nscore}<LSEP>[](symbol){sub.title}<LEND>[statement 62; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){results}
[](){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){$}<LSEP>[](symbol){x}<LSEP>[](symbol){data}<LEND>[](symbol){dat}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[argument 0; litteral](str){rbind}<LSEP>[](symbol){dat}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){dat}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The API returned NULL data.}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dat}<LSEP>[argument 1; litteral](str){accessed}<LEND>[](symbol){accessed}<LEND>[](symbol){dat}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.aggregate_data}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){data}<LSEP>[](symbol){link_maximum}<LSEP>[](symbol){conti}<LSEP>[](symbol){flow}<LSEP>[](symbol){origin}<LSEP>[](symbol){destination}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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; 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){$}<LSEP>[](symbol){data}<LSEP>[](symbol){conti}<LEND>[](symbol){}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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}
[](){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){$}<LSEP>[](symbol){all_dfs}<LSEP>[](symbol){id}<LEND>[statement 4; call](){}<LSEP>[](symbol){try_tibble}<LSEP>[](symbol){all_dfs}<LEND>[assign](){<-}<LSEP>[](symbol){rt_ticket_search}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){query}<LSEP>[](symbol){orderby}<LSEP>[](symbol){format}<LSEP>[](symbol){fields}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){format}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){l}<LSEP>[argument 1; litteral](str){s}<LSEP>[argument 2; litteral](str){i}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](logical){FALSE}<LSEP>[argument 1; litteral](str){Invalid choice of format, '}<LSEP>[](symbol){format}<LSEP>[argument 3; litteral](str){'. Valid options are l (long),...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){params}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){query}<LSEP>[](symbol){orderby}<LSEP>[](symbol){format}<LSEP>[](symbol){fields}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){url}<LEND>[call](){}<LSEP>[](symbol){rt_url}<LSEP>[argument 0; litteral](str){search}<LSEP>[argument 1; litteral](str){ticket}<LSEP>[](symbol){params}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){response}<LEND>[call](){}<LSEP>[](symbol){rt_GET}<LSEP>[](symbol){url}<LSEP>[](symbol){...}<LEND>[statement 4; call](){}<LSEP>[](symbol){stopforstatus}<LSEP>[](symbol){response}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<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 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){format}<LSEP>[argument 1; litteral](str){s}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[argument 1; litteral](str){\\n}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){parse_rt_properties}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){result}<LSEP>[](symbol){names}<LEND>[argument 1; call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){result}<LSEP>[](symbol){unlist}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){id}<LSEP>[argument 1; litteral](str){Subject}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){try_tibble}<LSEP>[](symbol){result}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){format}<LSEP>[argument 1; litteral](str){i}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stringr}<LSEP>[](symbol){str_split}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[argument 1; litteral](str){\n}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){Filter}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){r}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){r}<LEND>[argument 1; litteral](real){0.000000}<LEND>[](symbol){result}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){ticket/}<LSEP>[argument 1; litteral](str){}<LSEP>[](symbol){result}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){format}<LSEP>[argument 1; litteral](str){l}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){lapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){strsplit}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){response}<LSEP>[](symbol){body}<LEND>[argument 1; litteral](str){\\n\\n--\\n\\n}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){parse_rt_properties}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){tidy_long_search_result}<LSEP>[](symbol){result}<LEND>[](symbol){result}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.collapse.recursive}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){tloc}<LSEP>[](symbol){tpop}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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}
[](){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}
[](){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}
[](){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; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sqrt}<LSEP>[](symbol){vars}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<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; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){d}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){vars}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; 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}<LSEP>[](symbol){affin}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){check}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LSEP>[](symbol){var1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LSEP>[](symbol){var2}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){.Machine}<LSEP>[](symbol){double.eps}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){One of the sample variances is...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){affin}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){p}<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){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LEND>[argument 0; call](){}<LSEP>[](symbol){%%}<LSEP>[](symbol){var1}<LSEP>[](symbol){var2}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){det}<LSEP>[](symbol){vars}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<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; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){%%}<LEND>[argument 0; call](){}<LSEP>[](symbol){%%}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){d}<LEND>[argument 1; call](){}<LSEP>[](symbol){solve}<LSEP>[](symbol){vars}<LEND>[](symbol){d}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){sqrt}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<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}<LSEP>[](symbol){affin}
[](){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}
[](){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}
[](){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}
[](){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}
[](){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}
[](){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}
[](){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; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_c}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){s2}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_ave}<LSEP>[argument 1; 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){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<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){r}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){r}<LEND>[](symbol){s2}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[](symbol){h_ave}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n_ave}<LSEP>[argument 1; 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){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<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){r}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){r}<LEND>[](symbol){s2}<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>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n_ave}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){n_ave}<LEND>[](symbol){h_ave}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){h_ave}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){aNoCorr}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){n_ave}<LSEP>[](symbol){n_c}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){s2}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){bNoCorr}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){p_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<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){r}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){r}<LEND>[](symbol){s2}<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>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n_ave}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){n_ave}<LEND>[](symbol){h_ave}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){cNoCorr}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){h_ave}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){He}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[](symbol){p_ave}<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>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p_ave}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){FST}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){a}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){a}<LSEP>[](symbol){b}<LEND>[](symbol){c}<LEND>[statement 19; assign](){=}<LSEP>[](symbol){FSTNoCorr}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){aNoCorr}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){aNoCorr}<LSEP>[](symbol){bNoCorr}<LEND>[](symbol){cNoCorr}<LEND>[statement 20; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){He}<LSEP>[](symbol){FST}<LSEP>[](symbol){a}<LEND>[argument 3; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){a}<LSEP>[](symbol){b}<LEND>[](symbol){c}<LEND>[](symbol){FSTNoCorr}<LSEP>[](symbol){aNoCorr}<LEND>[argument 6; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){aNoCorr}<LSEP>[](symbol){bNoCorr}<LEND>[](symbol){cNoCorr}<LEND>[](symbol){p_ave}<LEND>[assign](){<-}<LSEP>[](symbol){utils.outflank.MakeDiploidFSTMat}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){SNPmat}<LSEP>[](symbol){locusNames}<LSEP>[](symbol){popNames}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){locusname}<LEND>[call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){locusNames}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){popname}<LEND>[call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){popNames}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){snplevs}<LEND>[call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){SNPmat}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){ls}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){snplevs}<LSEP>[argument 1; litteral](str){}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){ls}<LSEP>[argument 1; litteral](str){012}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){ls}<LSEP>[argument 1; litteral](str){0129}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LSEP>[argument 0; litteral](str){Error: Your snp matrix does no...}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){SNPmat}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){popname}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LSEP>[argument 0; litteral](str){Error: your population names d...}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){SNPmat}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){locusname}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LSEP>[argument 0; litteral](str){Error: your locus names do no...}<LEND>[statement 7; call](){}<LSEP>[](symbol){writeLines}<LSEP>[argument 0; litteral](str){Calculating FSTs, may take a f...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){nloci}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){locusname}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){FSTmat}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){nloci}<LSEP>[argument 2; litteral](real){8.000000}<LEND>[statement 10; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nloci}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){FSTmat}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){getFSTs_diploids}<LSEP>[](symbol){popname}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){SNPmat}<LSEP>[](symbol){}<LSEP>[](symbol){i}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){%%}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](real){10000.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){i}<LSEP>[argument 1; litteral](str){done of}<LSEP>[](symbol){nloci}<LEND>[statement 11; assign](){=}<LSEP>[](symbol){outTemp}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){FSTmat}<LEND>[statement 12; assign](){=}<LSEP>[](symbol){outTemp}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){locusname}<LSEP>[](symbol){outTemp}<LEND>[statement 13; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){outTemp}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){LocusName}<LSEP>[argument 1; litteral](str){He}<LSEP>[argument 2; litteral](str){FST}<LSEP>[argument 3; litteral](str){T1}<LSEP>[argument 4; litteral](str){T2}<LSEP>[argument 5; litteral](str){FSTNoCorr}<LSEP>[argument 6; litteral](str){T1NoCorr}<LSEP>[argument 7; litteral](str){T2NoCorr}<LSEP>[argument 8; litteral](str){meanAlleleFreq}<LEND>[statement 14; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){outTemp}<LEND>[assign](){=}<LSEP>[](symbol){getFSTs_diploids}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){popNameList}<LSEP>[](symbol){SNPDataColumn}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){popnames}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LSEP>[](symbol){popNameList}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){popNameTemp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){popnames}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){SNPDataColumn}<LSEP>[argument 1; litteral](real){9.000000}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){snpDataTemp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){SNPDataColumn}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){SNPDataColumn}<LSEP>[argument 1; litteral](real){9.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){HetCounts}<LEND>[call](){}<LSEP>[](symbol){tapply}<LSEP>[](symbol){snpDataTemp}<LEND>[argument 1; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){popNameTemp}<LSEP>[](symbol){snpDataTemp}<LEND>[](symbol){length}<LEND>[statement 4; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){HetCounts}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){HetCounts}<LEND>[litteral](real){0.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){HetCounts}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[argument 1; litteral](logical){NA}<LSEP>[argument 2; litteral](logical){NA}<LSEP>[argument 3; litteral](logical){NA}<LSEP>[argument 4; litteral](logical){NA}<LSEP>[argument 5; litteral](logical){NA}<LSEP>[argument 6; litteral](logical){NA}<LSEP>[argument 7; 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){dim}<LSEP>[](symbol){HetCounts}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){HetCounts}<LEND>[argument 1; litteral](str){}<LEND>[argument 1; litteral](str){01}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){HetCounts}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){HetCounts}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){HetCounts}<LEND>[argument 1; litteral](str){}<LEND>[argument 1; litteral](str){12}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){HetCounts}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){HetCounts}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){HetCounts}<LEND>[argument 1; litteral](str){}<LEND>[argument 1; litteral](str){02}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){HetCounts}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){HetCounts}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){HetCounts}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){WC_FST_Diploids_2Alleles}<LSEP>[](symbol){HetCounts}<LEND>[statement 8; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){out}
[](){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; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Single argument requires a pre...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){lm}<LSEP>[](symbol){x}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){y}<LEND>[statement 2; 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){ncol}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){y}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){missing}<LSEP>[](symbol){dist.method}<LEND>[true branch; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Argument dist.method does not ...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){proxy}<LSEP>[](symbol){pr_DB}<LEND>[](symbol){entry_exists}<LEND>[](symbol){dist.method}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){dist.method should be one of t...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){lm}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){proxy}<LSEP>[](symbol){dist}<LEND>[](symbol){x}<LSEP>[](symbol){y}<LSEP>[](symbol){dist.method}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){wfun}<LEND>[call](){}<LSEP>[](symbol){.canonicalizeWindowFunction}<LSEP>[](symbol){window.type}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dir}<LSEP>[](symbol){step.pattern}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){norm}<LEND>[call](){}<LSEP>[](symbol){attr}<LSEP>[](symbol){dir}<LSEP>[argument 1; litteral](str){norm}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[](symbol){partial}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Argument `partial' is obsolete...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){open.end}<LSEP>[litteral](logical){TRUE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){lm}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){lm}<LEND>[statement 8; control flow](){if}<LSEP>[](symbol){open.begin}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){\|\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){norm}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){norm}<LSEP>[argument 1; litteral](str){N}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Open-begin requires step patte...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){lm}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[](symbol){lm}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){np}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){precm}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){np}<LSEP>[](symbol){m}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){precm}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){}<LEND>[litteral](real){0.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){precm}<LSEP>[litteral](NULL){NULL}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){np}<LSEP>[](symbol){n}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){gcm}<LEND>[call](){}<LSEP>[](symbol){globalCostMatrix}<LSEP>[](symbol){lm}<LSEP>[](symbol){dir}<LSEP>[](symbol){wfun}<LSEP>[](symbol){precm}<LSEP>[](symbol){...}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){N}<LEND>[](symbol){n}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){M}<LEND>[](symbol){m}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){call}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){openEnd}<LEND>[](symbol){open.end}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){openBegin}<LEND>[](symbol){open.begin}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){windowFunction}<LEND>[](symbol){wfun}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){lastcol}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){costMatrix}<LEND>[](symbol){np}<LSEP>[](symbol){}<LEND>[statement 17; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){norm}<LEND>[true branch; block](){}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){norm}<LSEP>[argument 1; litteral](str){N+M}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lastcol}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){lastcol}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){m}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){norm}<LSEP>[argument 1; litteral](str){N}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lastcol}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){lastcol}<LSEP>[](symbol){n}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){norm}<LSEP>[argument 1; litteral](str){M}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lastcol}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){lastcol}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){m}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){jmin}<LEND>[](symbol){m}<LEND>[statement 19; control flow](){if}<LSEP>[](symbol){open.end}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){norm}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Open-end alignments require no...}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){jmin}<LEND>[call](){}<LSEP>[](symbol){which.min}<LSEP>[](symbol){lastcol}<LEND>[statement 20; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){distance}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){costMatrix}<LEND>[](symbol){np}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){jmin}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){distance}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){No warping path exists that is...}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){norm}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){normalizedDistance}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lastcol}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){jmin}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){normalizedDistance}<LEND>[litteral](logical){NA}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){distance.only}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mapping}<LEND>[call](){}<LSEP>[](symbol){backtrack}<LSEP>[](symbol){gcm}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){gcm}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){gcm}<LSEP>[](symbol){mapping}<LEND>[statement 24; control flow](){if}<LSEP>[](symbol){open.begin}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){index1}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){index1}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){index1s}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){index1s}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){index2}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){index2}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){index2s}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){index2s}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){lm}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lm}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){costMatrix}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){costMatrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){directionMatrix}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){directionMatrix}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){keep.internals}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){costMatrix}<LEND>[litteral](NULL){NULL}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){directionMatrix}<LEND>[litteral](NULL){NULL}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){localCostMatrix}<LEND>[](symbol){lm}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){y}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){query}<LEND>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){gcm}<LSEP>[](symbol){reference}<LEND>[](symbol){y}<LEND>[statement 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){gcm}<LEND>[litteral](str){dtw}<LEND>[statement 27; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){gcm}<LEND>[assign](){<-}<LSEP>[](symbol){is.dtw}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){d}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){d}<LSEP>[argument 1; litteral](str){dtw}<LEND>[assign](){<-}<LSEP>[](symbol){print.dtw}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){...}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){head}<LSEP>[litteral](str){DTW alignment object\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){size}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){Alignment size (query x refere...}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){N}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){M}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){call}<LEND>[call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){Call: %s\n}<LEND>[argument 1; call](){}<LSEP>[](symbol){deparse}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){call}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[](symbol){head}<LSEP>[](symbol){size}<LSEP>[](symbol){call}<LEND>[assign](){<-}<LSEP>[](symbol){.canonicalizeWindowFunction}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){w}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.function}<LSEP>[](symbol){w}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){w}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){wt}<LEND>[call](){}<LSEP>[](symbol){pmatch}<LSEP>[](symbol){w}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){none}<LSEP>[argument 1; litteral](str){sakoechiba}<LSEP>[argument 2; litteral](str){itakura}<LSEP>[argument 3; litteral](str){slantedband}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){wt}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Ambiguous or unsupported char ...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){wfun}<LEND>[call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){wt}<LSEP>[](symbol){noWindow}<LSEP>[](symbol){sakoeChibaWindow}<LSEP>[](symbol){itakuraWindow}<LSEP>[](symbol){slantedBandWindow}<LEND>[statement 4; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){wfun}
[](){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}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){as.folderh}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){classes}<LEND>[body; call](){}<LSEP>[](symbol){UseMethod}<LSEP>[argument 0; litteral](str){as.folderh}
[](){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){$}<LSEP>[](symbol){rf}<LSEP>[](symbol){popn}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){poppair}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){rfB}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){rf}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rf}<LSEP>[](symbol){popn}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){poppair}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<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){ Calculations based on allopa...}<LEND>[statement 11; control flow](){if}<LSEP>[](symbol){sympatric}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){rfA}<LSEP>[](symbol){rf}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rfB}<LSEP>[](symbol){rf}<LEND>[statement 2; 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){ Calculations based on sympat...}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){simA}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){pair}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){simB}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){pair}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){fd}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){pair}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){falsepos}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LSEP>[](symbol){reps}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){obs}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){fdmat}<LEND>[call](){}<LSEP>[](symbol){gl.fixed.diff}<LSEP>[](symbol){pair}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){obs}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){fdmat}<LSEP>[argument 1; litteral](real){2.000000}<LSEP>[argument 2; litteral](real){1.000000}<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){Calculating false positive rat...}<LSEP>[](symbol){reps}<LSEP>[argument 2; litteral](str){replications. 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; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){simA}<LSEP>[](symbol){i}<LEND>[litteral](logical){NA}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){simB}<LSEP>[](symbol){i}<LEND>[litteral](logical){NA}<LEND>[false branch; 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){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rfA}<LSEP>[](symbol){frequency}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){100.000000}<LEND>[](symbol){delta}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rfB}<LSEP>[](symbol){frequency}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){100.000000}<LEND>[](symbol){delta}<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){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rfB}<LSEP>[](symbol){frequency}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){100.000000}<LEND>[](symbol){delta}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rfA}<LSEP>[](symbol){frequency}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){100.000000}<LEND>[](symbol){delta}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){simA}<LSEP>[](symbol){i}<LEND>[litteral](logical){NA}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){simB}<LSEP>[](symbol){i}<LEND>[litteral](logical){NA}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){szA}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rfA}<LSEP>[](symbol){nobs}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){szB}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rfB}<LSEP>[](symbol){nobs}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){pbA}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rfA}<LSEP>[](symbol){frequency}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){pbB}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){rfB}<LSEP>[](symbol){frequency}<LEND>[](symbol){i}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){simA}<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){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; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){simB}<LSEP>[](symbol){i}<LEND>[](symbol){szB}<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){simA}<LSEP>[](symbol){i}<LEND>[](symbol){szA}<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>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){simB}<LSEP>[](symbol){i}<LEND>[](symbol){szB}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){falsepos}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){fd}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){mn}<LEND>[call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){falsepos}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){sdev}<LEND>[call](){}<LSEP>[](symbol){sd}<LSEP>[](symbol){falsepos}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){nprob}<LEND>[call](){}<LSEP>[](symbol){pnorm}<LSEP>[](symbol){obs}<LSEP>[](symbol){mn}<LSEP>[](symbol){sdev}<LSEP>[argument 3; litteral](logical){FALSE}<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}<LSEP>[argument 0; litteral](str){Threshold minor allele frequen...}<LSEP>[](symbol){delta}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Estimated mean count of false ...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; 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}
[](){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}
[](){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}
[](){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}
[](){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}
[](){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; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Error: At this time }<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cl}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 2; litteral](str){ must have 2 levels}<LSEP>[argument 3; litteral](str){}<LEND>[statement 15; assign](){=}<LSEP>[](symbol){extraArgs}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){...}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){extraArgs}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){arg}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){formals}<LSEP>[](symbol){rpart}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){indx}<LEND>[call](){}<LSEP>[](symbol){match}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){extraArgs}<LEND>[](symbol){arg}<LSEP>[argument 2; litteral](real){0.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){indx}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Error: Argument}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){extraArgs}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){indx}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 2; litteral](str){not matched}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){ny}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.factor}<LSEP>[](symbol){y}<LEND>[statement 18; control flow](){if}<LSEP>[](symbol){test.dat}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){test.y}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.factor}<LSEP>[](symbol){test.y}<LEND>[statement 19; assign](){=}<LSEP>[](symbol){method}<LSEP>[litteral](str){class}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){discrete}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){predict.type}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){f}<LSEP>[](symbol){dat}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){predict}<LSEP>[](symbol){f}<LSEP>[](symbol){dat}<LSEP>[argument 2; litteral](str){class}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LSEP>[](symbol){p}<LEND>[](symbol){p}<LEND>[](symbol){a}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){real}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){predict.type}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){f}<LSEP>[](symbol){dat}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){predict}<LSEP>[](symbol){f}<LSEP>[](symbol){dat}<LSEP>[argument 2; litteral](str){prob}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ind}<LEND>[call](){}<LSEP>[](symbol){\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){a}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){a}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){ind}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){a}<LSEP>[](symbol){ind}<LEND>[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){a}<LSEP>[](symbol){ind}<LEND>[argument 1; litteral](real){0.000100}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){a}<LSEP>[](symbol){ind}<LEND>[argument 1; litteral](real){0.999900}<LEND>[statement 3; assign](){=}<LSEP>[](symbol){f}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){0.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){log}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){a}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){a}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){f}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; assign](){=}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){f}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.nan}<LSEP>[](symbol){f}<LEND>[litteral](real){0.510000}<LEND>[](symbol){f}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){gentle}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){predict.type}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){f}<LSEP>[](symbol){dat}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){predict}<LSEP>[](symbol){f}<LSEP>[](symbol){dat}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){method}<LSEP>[litteral](str){anova}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){wfun}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){yf}<LSEP>[](symbol){f}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){yf}<LEND>[](symbol){f}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){loss}<LSEP>[argument 1; litteral](str){logistic}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wfun}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){yf}<LSEP>[](symbol){f}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){yf}<LEND>[](symbol){f}<LEND>[statement 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){a}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){a}<LEND>[statement 25; assign](){=}<LSEP>[](symbol){coefs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){wts}<LSEP>[](symbol){eta}<LSEP>[](symbol){yf}<LSEP>[](symbol){alp}<LEND>[body; block](){}<LSEP>[statement 0; litteral](real){1.000000}<LEND>[statement 26; control flow](){if}<LSEP>[](symbol){model.coef}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){loss}<LSEP>[argument 1; litteral](str){exponential}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](str){discrete}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){coefs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){wts}<LSEP>[](symbol){eta}<LSEP>[](symbol){yf}<LSEP>[](symbol){alp}<LEND>[body; block](){}<LSEP>[](symbol){alp}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){coefs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){wts}<LSEP>[](symbol){eta}<LSEP>[](symbol){yf}<LSEP>[](symbol){alp}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){alpst}<LSEP>[](symbol){alp}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){max.iter}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){alp0}<LSEP>[](symbol){alp}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){pval}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){wts}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){yf}<LEND>[](symbol){eta}<LEND>[](symbol){alp}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){m11}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){eta}<LSEP>[](symbol){pval}<LEND>[](symbol){eta}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){m12}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){yf}<LSEP>[](symbol){pval}<LEND>[](symbol){eta}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){m11}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){alp}<LSEP>[](symbol){alpst}<LEND>[statement 1; control flow](){break}<LEND>[statement 5; assign](){=}<LSEP>[](symbol){alp}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){alp}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){m12}<LSEP>[](symbol){m11}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){a1}<LEND>[call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){alp}<LSEP>[](symbol){alp0}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){a1}<LSEP>[](symbol){delta}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){break}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){verbose}<LEND>[true branch; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){FINAL: iter=}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){ rate=}<LSEP>[](symbol){a1}<LSEP>[argument 4; litteral](str){\n}<LEND>[](symbol){alp}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){coefs}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){wts}<LSEP>[](symbol){eta}<LSEP>[](symbol){yf}<LSEP>[](symbol){alp}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){alpst}<LSEP>[](symbol){alp}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){max.iter}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){alp0}<LSEP>[](symbol){alp}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){pval}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){wts}<LEND>[argument 1; call](){}<LSEP>[](symbol){exp}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){yf}<LEND>[](symbol){eta}<LEND>[](symbol){alp}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){pval}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<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){+}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){pval}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){m11}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){eta}<LSEP>[](symbol){pval}<LEND>[](symbol){eta}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){m12}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){yf}<LSEP>[](symbol){pval}<LEND>[](symbol){eta}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){m11}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){alp}<LSEP>[](symbol){alpst}<LEND>[statement 1; control flow](){break}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){alp}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){alp}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){m12}<LSEP>[](symbol){m11}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){a1}<LEND>[call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){alp}<LSEP>[](symbol){alp0}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){a1}<LSEP>[](symbol){delta}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){break}<LEND>[statement 9; assign](){=}<LSEP>[](symbol){alp}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){alp}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){m12}<LSEP>[](symbol){m11}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){verbose}<LEND>[true branch; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){FINAL: iter=}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){ rate=}<LSEP>[](symbol){a1}<LSEP>[argument 4; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){alp}<LEND>[statement 27; assign](){=}<LSEP>[](symbol){lossObj}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){coefs}<LSEP>[](symbol){wfun}<LSEP>[](symbol){predict.type}<LSEP>[](symbol){method}<LSEP>[](symbol){type}<LSEP>[](symbol){loss}<LSEP>[](symbol){bag.shift}<LEND>[statement 28; assign](){=}<LSEP>[](symbol){result}<LEND>[call](){}<LSEP>[](symbol){ada.machine}<LSEP>[](symbol){x}<LSEP>[](symbol){ny}<LSEP>[](symbol){test.x}<LSEP>[](symbol){test.y}<LSEP>[](symbol){iter}<LSEP>[](symbol){nu}<LSEP>[](symbol){bag.frac}<LSEP>[](symbol){lossObj}<LSEP>[argument 8; litteral](NULL){NULL}<LSEP>[](symbol){na.action}<LSEP>[](symbol){...}<LEND>[statement 29; assign](){=}<LSEP>[](symbol){g}<LEND>[call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){lev}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.factor}<LEND>[argument 0; call](){}<LSEP>[](symbol){sign}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){result}<LSEP>[](symbol){F}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 30; assign](){=}<LSEP>[](symbol){tab}<LEND>[call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.factor}<LSEP>[](symbol){y}<LEND>[](symbol){g}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){True value}<LSEP>[argument 1; litteral](str){Final Prediction}<LEND>[statement 31; assign](){<-}<LSEP>[](symbol){nm}<LEND>[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){dim}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 32; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){nm}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){x}<LEND>[statement 33; assign](){=}<LSEP>[](symbol){obj}<LEND>[call](){}<LSEP>[](symbol){structure}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){result}<LSEP>[](symbol){g}<LSEP>[](symbol){cl}<LSEP>[](symbol){tab}<LSEP>[](symbol){iter}<LEND>[argument 5; call](){}<LSEP>[](symbol){as.vector}<LSEP>[](symbol){y}<LEND>[](symbol){nu}<LEND>[argument 7; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){x}<LEND>[](symbol){nm}<LSEP>[](symbol){bag.frac}<LSEP>[](symbol){na.action}<LEND>[argument 1; litteral](str){ada}<LEND>[](symbol){obj}
[](){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}
[](){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; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Fatal Error: genlight object r...}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ploidy}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; 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){method}<LSEP>[argument 1; litteral](str){pop}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){ind}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Method must either be...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){method}<LSEP>[litteral](str){pop}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){n.invariant}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Number of invariant l...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){n.invariant}<LSEP>[litteral](real){0.000000}<LEND>[statement 10; 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){boxplot}<LSEP>[argument 1; litteral](str){standard}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){boxplot}<LSEP>[argument 1; litteral](str){adjusted}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Warning: Box-whisker plots mus...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){boxplot}<LSEP>[litteral](str){adjusted}<LEND>[statement 11; 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){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: genlight object con...}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){pop}<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){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){ No population assignments de...}<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 1; assign](){<-}<LSEP>[](symbol){sgl}<LEND>[call](){}<LSEP>[](symbol){seppop}<LSEP>[](symbol){x}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating Observed Heteroz...}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){Ho}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){sgl}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){colMeans}<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>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){nl}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){sgl}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colSums}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){Ho.adj}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){Ho}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[](symbol){n.invariant}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){sums}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){sgl}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){colSums}<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>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){sums}<LSEP>[](symbol){Ho}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){n}<LEND>[](symbol){n}<LSEP>[](symbol){nl}<LEND>[argument 3; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[](symbol){n.invariant}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){df1}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){Ho}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){Ho}<LEND>[argument 2; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){Ho.adj}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){df2}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){n}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){df2}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){pop}<LSEP>[argument 1; litteral](str){nInd}<LSEP>[argument 2; litteral](str){nLoc}<LSEP>[argument 3; litteral](str){nLoc.adj}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){plyr}<LSEP>[](symbol){join}<LEND>[](symbol){df1}<LSEP>[](symbol){df2}<LSEP>[argument 2; litteral](str){pop}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating Expected Heteroz...}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){Hexp}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){sgl}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){Hexp.adj}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){sgl}<LEND>[statement 16; 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){sgl}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){sgl}<LSEP>[](symbol){i}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){utils.recalc.freqhomref}<LSEP>[](symbol){gl}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){utils.recalc.freqhomsnp}<LSEP>[](symbol){gl}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){gl}<LEND>[call](){}<LSEP>[](symbol){utils.recalc.freqhets}<LSEP>[](symbol){gl}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){p}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){FreqHomRef}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){q}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){FreqHomSnp}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){hets}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){gl}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){FreqHets}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){p}<LEND>[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){2.000000}<LSEP>[](symbol){p}<LEND>[](symbol){hets}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){q}<LEND>[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){2.000000}<LSEP>[](symbol){q}<LEND>[](symbol){hets}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){H}<LEND>[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){p}<LSEP>[](symbol){p}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){q}<LSEP>[](symbol){q}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Hexp}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){H}<LSEP>[](symbol){T}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Hexp.adj}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Hexp}<LSEP>[](symbol){i}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[](symbol){n.invariant}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[](symbol){nl}<LSEP>[](symbol){n.invariant}<LEND>[argument 4; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 5; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho.adj}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 6; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){Hexp}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[argument 7; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){Hexp.adj}<LSEP>[argument 1; litteral](real){6.000000}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){pop}<LSEP>[argument 1; litteral](str){nInd}<LSEP>[argument 2; litteral](str){nLoc}<LSEP>[argument 3; litteral](str){nLoc.inv}<LSEP>[argument 4; litteral](str){Ho}<LSEP>[argument 5; litteral](str){Ho.adj}<LSEP>[argument 6; litteral](str){He}<LSEP>[argument 7; litteral](str){He.adj}<LEND>[statement 19; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){op}<LEND>[call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){0.000000}<LEND>[argument 2; litteral](str){m}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){n.invariant}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){df.ordered}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[](symbol){}<LEND>[statement 1; call](){}<LSEP>[](symbol){barplot}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){Ho}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){pop}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){nInd}<LEND>[argument 2; litteral](str){ \| }<LEND>[argument 2; litteral](real){2.000000}<LSEP>[](symbol){cex.labels}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[](symbol){F}<LEND>[argument 6; call](){}<LSEP>[](symbol){rainbow}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){df.ordered}<LEND>[argument 7; litteral](str){Observed Heterozygosity by Pop...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){df.ordered}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){He}<LEND>[](symbol){}<LEND>[statement 3; call](){}<LSEP>[](symbol){barplot}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){He}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){pop}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){nInd}<LEND>[argument 2; litteral](str){ \| }<LEND>[argument 2; litteral](real){2.000000}<LSEP>[](symbol){cex.labels}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[](symbol){F}<LEND>[argument 6; call](){}<LSEP>[](symbol){rainbow}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){df.ordered}<LEND>[argument 7; litteral](str){Expected Heterozygosity by Pop...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){df.ordered}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho.adj}<LEND>[](symbol){}<LEND>[statement 1; call](){}<LSEP>[](symbol){barplot}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){Ho.adj}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){pop}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){nInd}<LEND>[argument 2; litteral](str){ \| }<LEND>[argument 2; litteral](real){2.000000}<LSEP>[](symbol){cex.labels}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[](symbol){F}<LEND>[argument 6; call](){}<LSEP>[](symbol){rainbow}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){df.ordered}<LEND>[argument 7; litteral](str){Observed Heterozygosity by Pop...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){df.ordered}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){He.adj}<LEND>[](symbol){}<LEND>[statement 3; call](){}<LSEP>[](symbol){barplot}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){He.adj}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){pop}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df.ordered}<LSEP>[](symbol){nInd}<LEND>[argument 2; litteral](str){ \| }<LEND>[argument 2; litteral](real){2.000000}<LSEP>[](symbol){cex.labels}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[](symbol){F}<LEND>[argument 6; call](){}<LSEP>[](symbol){rainbow}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){df.ordered}<LEND>[argument 7; litteral](str){Expected Heterozygosity by Pop...}<LEND>[statement 20; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Reporting Heterozygosity by ...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n No. of loci =}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of individuals =}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No. of populations =}<LEND>[argument 1; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Miniumum Observed Heterozy...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){n.invariant}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ [Corrected:}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho.adj}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 2; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 6; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Maximum Observed Heterozyg...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){n.invariant}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ [Corrected:}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho.adj}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 2; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 8; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Average Observed Heterozyg...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){n.invariant}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ [Corrected:}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho.adj}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 2; litteral](str){]\n\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\n}<LEND>[statement 10; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Miniumum Expected Heterozy...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){He}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){n.invariant}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ [Corrected:}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){He.adj}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 2; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 12; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Maximum Expected Heterozyg...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){He}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){n.invariant}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ [Corrected:}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){He.adj}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 2; litteral](str){]\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n}<LEND>[statement 14; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Average Expected Heterozyg...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){He}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){n.invariant}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ [Corrected:}<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){He.adj}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; litteral](real){6.000000}<LEND>[argument 2; litteral](str){]\n\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){\n\n}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){n.invariant}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Average correction factor fo...}<LEND>[argument 1; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[](symbol){n.invariant}<LEND>[argument 2; litteral](str){\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Heterozygosity estimates not...}<LEND>[statement 17; 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){n.invariant}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){df}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){df}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){pop}<LSEP>[argument 1; litteral](str){nInd}<LSEP>[argument 2; litteral](str){nLoc}<LSEP>[argument 3; litteral](str){Ho}<LSEP>[argument 4; litteral](str){He}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){ind}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Calculating observed heteroz...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Note: No adjustment for inva...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){c.na}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){c.hets}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){c.hom0}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){c.hom2}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[statement 6; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){c.na}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){c.hets}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){c.na}<LSEP>[](symbol){i}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){c.hom0}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){c.na}<LSEP>[](symbol){i}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){c.hom2}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){m}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){c.na}<LSEP>[](symbol){i}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){cbind.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){ind.names}<LEND>[](symbol){c.hets}<LSEP>[](symbol){c.hom0}<LSEP>[](symbol){c.hom2}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){ind.name}<LSEP>[argument 1; litteral](str){Ho}<LSEP>[argument 2; litteral](str){f.hom.ref}<LSEP>[argument 3; litteral](str){f.hom.alt}<LEND>[statement 9; control flow](){if}<LSEP>[](symbol){plot}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){op}<LEND>[call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[argument 1; litteral](real){0.500000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[argument 2; litteral](str){m}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){boxplot}<LSEP>[argument 1; litteral](str){standard}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whisker}<LEND>[call](){}<LSEP>[](symbol){boxplot}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](str){red}<LSEP>[](symbol){range}<LSEP>[argument 4; litteral](str){Heterozygosity by Individual}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Standard boxplot, no adjustm...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outliers}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[argument 0; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){ind.name}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Standard boxplot, no adjustm...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){whisker}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){robustbase}<LSEP>[](symbol){adjbox}<LEND>[](symbol){df}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](str){red}<LSEP>[](symbol){range}<LSEP>[argument 5; litteral](str){Heterozygosity by Individual}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Boxplot adjusted to account ...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){outliers}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){ind.name}<LEND>[argument 1; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){Ho}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Boxplot adjusted to account ...}<LEND>[statement 2; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){c.hets}<LSEP>[argument 1; litteral](str){red}<LSEP>[argument 2; litteral](NULL){NULL}<LSEP>[argument 3; litteral](real){100.000000}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Reporting Heterozygosity by In...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){No. of loci =}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){No. of individuals =}<LEND>[argument 1; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Miniumum Observed Heterozygo...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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){$}<LSEP>[](symbol){whisker}<LSEP>[](symbol){out}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ No outliers detected\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Outliers detected -- \n}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){outliers}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){par}<LSEP>[](symbol){op}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 16; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){df}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){utils.recalc.avgpic}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){hold}<LSEP>[](symbol){x}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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; 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; 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, lo...}<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){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){monomorphs}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Dataset contains mo...}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){ calculations\n}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SNP}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){AvgPIC}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){AvgPIC}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Locus metric AvgPIC does not...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatioRef}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatioRef}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Locus metric OneRatioRef doe...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatioSnp}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatioSnp}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Locus metric OneRatioSnp doe...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){PICRef}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){PICRef}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Locus metric PICRef does not...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){PICSnp}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){PICSnp}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Locus metric PICSnp does not...}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SilicoDArT}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){PIC}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){PIC}<LEND>[call](){}<LSEP>[](symbol){array}<LSEP>[argument 0; litteral](logical){NA}<LEND>[argument 1; call](){}<LSEP>[](symbol){nLoc}<LSEP>[](symbol){x}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Locus metric PIC does not ex...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatio}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatio}<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 OneRatio does n...}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){t}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SNP}<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){ Recalculating OneRatioRef, O...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){c0}<LEND>[call](){}<LSEP>[](symbol){colSums}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[](symbol){T}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){c1}<LEND>[call](){}<LSEP>[](symbol){colSums}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){T}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){c2}<LEND>[call](){}<LSEP>[](symbol){colSums}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){T}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){c}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){c0}<LSEP>[](symbol){c1}<LEND>[](symbol){c2}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatioRef}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){c0}<LSEP>[](symbol){c1}<LEND>[](symbol){c}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){OneRatioRef}<LEND>[litteral](logical){TRUE}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatioSnp}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){c1}<LSEP>[](symbol){c2}<LEND>[](symbol){c}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){OneRatioSnp}<LEND>[litteral](logical){TRUE}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){OneRatioRef}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatioRef}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){OneRatioSnp}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatioSnp}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){ZeroRatioRef}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){OneRatioRef}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){ZeroRatioSnp}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){OneRatioSnp}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){PICRef}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){OneRatioRef}<LSEP>[](symbol){OneRatioRef}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){ZeroRatioRef}<LSEP>[](symbol){ZeroRatioRef}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){PICRef}<LEND>[litteral](logical){TRUE}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){PICSnp}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){OneRatioSnp}<LSEP>[](symbol){OneRatioSnp}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){ZeroRatioSnp}<LSEP>[](symbol){ZeroRatioSnp}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){PICSnp}<LEND>[litteral](logical){TRUE}<LEND>[statement 17; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){AvgPIC}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){PICRef}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){PICSnp}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 18; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){AvgPIC}<LEND>[litteral](logical){TRUE}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SilicoDArT}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Recalculating OneRatio, PIC\n}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){OneRatio}<LEND>[call](){}<LSEP>[](symbol){colMeans}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){t}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){T}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){OneRatio}<LEND>[](symbol){OneRatio}<LEND>[statement 3; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){OneRatio}<LEND>[litteral](logical){TRUE}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){ZeroRatio}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){OneRatio}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics}<LEND>[](symbol){PIC}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){OneRatio}<LSEP>[](symbol){OneRatio}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){ZeroRatio}<LSEP>[](symbol){ZeroRatio}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){loc.metrics.flags}<LEND>[](symbol){PIC}<LEND>[litteral](logical){TRUE}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Completed:}<LSEP>[](symbol){funname}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 15; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.pcoa}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){nfactors}<LSEP>[](symbol){correction}<LSEP>[](symbol){parallel}<LSEP>[](symbol){n.cores}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){funname}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){match.call}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){build}<LSEP>[litteral](str){Jacob}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){genlight}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){verbose}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){verbose}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){fd}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){gl}<LEND>[statement 1; 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 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){dist}<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; assign](){<-}<LSEP>[](symbol){verbose}<LSEP>[litteral](real){2.000000}<LEND>[statement 5; 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 6; 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 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; 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>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){dist}<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 Distance Matrix...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data.type}<LSEP>[litteral](str){dist}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](str){fd}<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 genlight object...}<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: Expecting either ...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){correction}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){correction}<LSEP>[litteral](str){none}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){correction}<LEND>[call](){}<LSEP>[](symbol){tolower}<LSEP>[](symbol){correction}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){correction}<LSEP>[argument 1; litteral](str){lingoes}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){correction}<LSEP>[argument 1; litteral](str){cailliez}<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: Correction if speci...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){correction}<LSEP>[litteral](str){none}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){dist}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){D}<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; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){correction}<LSEP>[argument 1; litteral](str){none}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Performing a PCoA, individua...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){title}<LSEP>[litteral](str){PCoA on Distance Matrix (no co...}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Performing a PCoA, individua...}<LSEP>[](symbol){correction}<LSEP>[argument 2; litteral](str){correction for stress (-ive ei...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){title}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){PCoA on Distance Matrix(}<LSEP>[](symbol){correction}<LSEP>[argument 2; litteral](str){)\nScree Plot (informative axe...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){pco}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ape}<LSEP>[](symbol){pcoa}<LEND>[](symbol){D}<LSEP>[](symbol){correction}<LEND>[argument 2; call](){}<LSEP>[](symbol){labels}<LSEP>[](symbol){D}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){correction}<LSEP>[argument 1; litteral](str){none}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eig.raw}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pco}<LSEP>[](symbol){values}<LEND>[](symbol){Eigenvalues}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){eig.raw}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pco}<LSEP>[](symbol){values}<LEND>[](symbol){Corr_eig}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){eig.raw.pos}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){eig.raw}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){eig.raw.pos.pc}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){eig.raw.pos}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){eig.raw.pos}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){eig.top}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw.pos}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){eig.raw.pos}<LEND>[argument 1; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){eig.raw.pos}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){eig.top.pc}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){eig.top}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){eig.raw.pos}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){eig.raw.noise}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){eig.raw}<LEND>[argument 1; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){eig.raw}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){eig.raw}<LSEP>[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; assign](){<-}<LSEP>[](symbol){problem}<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){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){eig.raw}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Some eigenvalues ne...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){problem}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){% of the mean eigenvalue for P...}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Tolerable negative eigenva...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){problem}<LSEP>[argument 1; litteral](real){20.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ If the stress (negative ei...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ (a) Apply more stringent f...}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ (b) Select an alternate di...}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ (c) Apply a transformation...}<LEND>[statement 4; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ (d) Interpret the visual r...}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){correction}<LSEP>[argument 1; litteral](str){lingoes}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){correction}<LSEP>[argument 1; litteral](str){cailliez}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Correction}<LSEP>[](symbol){correction}<LSEP>[argument 2; litteral](str){applied to remove negative eig...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Uncorrected ordination yielded}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){eig.top}<LEND>[argument 2; litteral](str){informative dimensions from}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 4; litteral](str){original dimensions\n}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ Ordination yielded}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){eig.top}<LEND>[argument 2; litteral](str){informative dimensions from}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){D}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 4; litteral](str){original dimensions\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ PCoA Axis 1 explains}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw.pos.pc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){% of the total variance\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ PCoA Axis 1 and 2 combined...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw.pos.pc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw.pos.pc}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){% of the total variance\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ PCoA Axis 1-3 combined exp...}<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){[}<LSEP>[](symbol){eig.raw.pos.pc}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw.pos.pc}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw.pos.pc}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){% of the total variance\n}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){p.object}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p.object}<LSEP>[](symbol){scores}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pco}<LSEP>[](symbol){vectors}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nfactors}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p.object}<LSEP>[](symbol){eig}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pco}<LSEP>[](symbol){values}<LEND>[](symbol){Eigenvalues}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p.object}<LSEP>[](symbol){loadings}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pco}<LSEP>[](symbol){vectors.cor}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nfactors}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p.object}<LSEP>[](symbol){call}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){\|\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SNP}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SilicoDArT}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SNP}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Performing a PCA, individual...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){title}<LSEP>[litteral](str){PCA on SNP Genotypes\nScree Pl...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SilicoDArT}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Performing a PCA, individual...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){title}<LSEP>[litteral](str){PCA on Tag P/A Data\nScree Plo...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pca}<LEND>[call](){}<LSEP>[](symbol){glPca}<LSEP>[](symbol){x}<LSEP>[](symbol){nfactors}<LSEP>[](symbol){parallel}<LSEP>[](symbol){n.cores}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){eig.raw}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pca}<LSEP>[](symbol){eig}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){eig.raw.pos}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){eig.raw}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){eig.raw.pos.pc}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){eig.raw.pos}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){eig.raw.pos}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){eig.top}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw.pos}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){eig.raw.pos}<LEND>[argument 1; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){eig.raw.pos}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){eig.top.pc}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){eig.top}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){eig.raw.pos}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){eig.raw.noise}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw}<LEND>[argument 1; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){eig.raw}<LEND>[argument 1; call](){}<LSEP>[](symbol){mean}<LSEP>[](symbol){eig.raw}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){eig.raw}<LSEP>[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; assign](){<-}<LSEP>[](symbol){problem}<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){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){eig.raw}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){mean}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){eig.raw}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](real){100.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Warning: Some eigenvalues ne...}<LEND>[argument 1; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){problem}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){% of the mean eigenvalue for P...}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ Tolerable negative eigenva...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){problem}<LSEP>[argument 1; litteral](real){20.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ If the stress (negative ei...}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ (a) Apply more stringent f...}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ (b) Undertake a PCoA with ...}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){ (c) Interperate the visual...}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){e}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pca}<LSEP>[](symbol){eig}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pca}<LSEP>[](symbol){eig}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pca}<LSEP>[](symbol){eig}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pca}<LSEP>[](symbol){eig}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){e}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LSEP>[](symbol){e}<LSEP>[argument 1; litteral](real){100.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pca}<LSEP>[](symbol){eig}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 11; 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){ Ordination yielded}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){e}<LEND>[argument 2; litteral](str){informative dimensions from}<LEND>[argument 3; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nInd}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 4; litteral](str){original dimensions\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ PCA Axis 1 explains}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){e}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){% of the total variance\n}<LEND>[statement 2; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ PCA Axis 1 and 2 combined ...}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){e}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){e}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 2; litteral](str){% of the total variance\n}<LEND>[statement 3; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){ PCA Axis 1-3 combined explain}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){e}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){e}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){e}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 2; litteral](str){% of the total variance\n}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){p.object}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p.object}<LSEP>[](symbol){scores}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pca}<LSEP>[](symbol){scores}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p.object}<LSEP>[](symbol){eig}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pca}<LSEP>[](symbol){eig}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p.object}<LSEP>[](symbol){loadings}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){pca}<LSEP>[](symbol){loadings}<LEND>[statement 16; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){p.object}<LSEP>[](symbol){call}<LEND>[call](){}<LSEP>[](symbol){match.call}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){op}<LEND>[call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[argument 1; litteral](real){0.500000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[argument 3; litteral](str){m}<LEND>[statement 12; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){seq}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){eig.top.pc}<LEND>[](symbol){eig.top.pc}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){m}<LEND>[statement 15; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){eigenvalue}<LSEP>[argument 1; litteral](str){percent}<LEND>[statement 16; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){data.type}<LSEP>[argument 1; litteral](str){SNP}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlab}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){PCA Axis}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xlab}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){PCoA Axis}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){ylab}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){Percentage Contribution}<LEND>[statement 18; call](){}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){eigenvalue}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){percent}<LEND>[argument 2; litteral](str){red}<LSEP>[](symbol){title}<LSEP>[argument 4; litteral](str){o}<LSEP>[](symbol){xlab}<LSEP>[](symbol){ylab}<LEND>[statement 19; call](){}<LSEP>[](symbol){abline}<LSEP>[argument 0; litteral](real){10.000000}<LSEP>[argument 1; litteral](str){blue}<LEND>[statement 20; call](){}<LSEP>[](symbol){par}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){0.500000}<LSEP>[argument 3; litteral](real){0.500000}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){eig.raw}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){main}<LSEP>[litteral](str){Noise Axes -- Warning: some ei...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){main}<LSEP>[litteral](str){Noise Axes -- all eigenvalues ...}<LEND>[statement 22; call](){}<LSEP>[](symbol){hist}<LSEP>[](symbol){eig.raw.noise}<LSEP>[](symbol){main}<LSEP>[argument 2; litteral](str){Eigenvalue}<LSEP>[argument 3; litteral](str){red}<LSEP>[argument 4; litteral](real){100.000000}<LEND>[statement 23; call](){}<LSEP>[](symbol){abline}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](str){blue}<LSEP>[argument 2; litteral](real){2.000000}<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){par}<LSEP>[](symbol){op}<LEND>[statement 26; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){class}<LSEP>[](symbol){p.object}<LEND>[litteral](str){glPca}<LEND>[statement 27; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){p.object}
[](){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; litteral](str){Compressing index rda files:}<LEND>[statement 17; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tools}<LSEP>[](symbol){resaveRdaFiles}<LEND>[argument 0; litteral](str){data/fileIndex.rda}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 18; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){1}<LEND>[statement 19; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tools}<LSEP>[](symbol){resaveRdaFiles}<LEND>[argument 0; litteral](str){data/metaIndex.rda}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 20; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){2}<LEND>[statement 21; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tools}<LSEP>[](symbol){resaveRdaFiles}<LEND>[argument 0; litteral](str){data/geoIndex.rda}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 22; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){3}<LEND>[statement 23; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tools}<LSEP>[](symbol){resaveRdaFiles}<LEND>[argument 0; litteral](str){data/gridIndex.rda}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 24; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){4\n}<LEND>[statement 25; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Checking rda file contents...}<LEND>[statement 26; assign](){<-}<LSEP>[](symbol){fileIndex2}<LEND>[call](){}<LSEP>[](symbol){read.table}<LSEP>[argument 0; litteral](str){DWDdata/fileIndex.txt}<LSEP>[argument 1; litteral](str){\t}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](str){character}<LEND>[statement 27; call](){}<LSEP>[](symbol){stopifnot}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){fileIndex}<LSEP>[](symbol){fileIndex2}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){metaIndex2}<LEND>[call](){}<LSEP>[](symbol){read.table}<LSEP>[argument 0; litteral](str){DWDdata/metaIndex.txt}<LSEP>[argument 1; litteral](str){\t}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 29; call](){}<LSEP>[](symbol){stopifnot}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){metaIndex}<LSEP>[](symbol){metaIndex2}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){geoIndex2}<LEND>[call](){}<LSEP>[](symbol){read.table}<LSEP>[argument 0; litteral](str){DWDdata/geoIndex.txt}<LSEP>[argument 1; litteral](str){\t}<LSEP>[argument 2; litteral](logical){TRUE}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 31; call](){}<LSEP>[](symbol){stopifnot}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){geoIndex}<LSEP>[](symbol){geoIndex2}<LEND>[statement 32; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){Reading subdaily/standard_form...}<LEND>[statement 33; 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){ }<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){°}<LSEP>[argument 1; litteral](str){degree}<LSEP>[](symbol){format_html}<LEND>[statement 39; assign](){<-}<LSEP>[](symbol){format_html}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){format_html}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){Formatbeschreibung}<LSEP>[](symbol){format_html}<LEND>[statement 40; assign](){<-}<LSEP>[](symbol){formatIndex}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){XML}<LSEP>[](symbol){readHTMLTable}<LEND>[](symbol){format_html}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 41; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){formatIndex}<LSEP>[](symbol){dividebyten}<LEND>[call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){0.1}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){formatIndex}<LSEP>[](symbol){Einheit}<LEND>[statement 42; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){formatIndex}<LSEP>[](symbol){Einheit}<LEND>[call](){}<LSEP>[](symbol){gsub}<LSEP>[argument 0; litteral](str){0.1 }<LSEP>[argument 1; litteral](str){}<LEND>[argument 2; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){formatIndex}<LSEP>[](symbol){Einheit}<LEND>[statement 43; call](){}<LSEP>[](symbol){save}<LSEP>[](symbol){formatIndex}<LSEP>[argument 1; litteral](str){data/formatIndex.rda}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 44; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){tools}<LSEP>[](symbol){resaveRdaFiles}<LEND>[argument 0; litteral](str){data/formatIndex.rda}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 45; call](){}<LSEP>[](symbol){messaget}<LSEP>[argument 0; litteral](str){Checking readVars parameter ab...}<LEND>[statement 46; assign](){<-}<LSEP>[](symbol){urls}<LEND>[call](){}<LSEP>[](symbol){selectDWD}<LSEP>[argument 0; litteral](str){Potsdam}<LSEP>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LSEP>[argument 4; litteral](logical){TRUE}<LSEP>[](symbol){metaIndex}<LSEP>[](symbol){fileIndex}<LEND>[statement 47; assign](){<-}<LSEP>[](symbol){urls}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){urls}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){1*_minute}<LSEP>[](symbol){urls}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){meta_data}<LSEP>[](symbol){urls}<LEND>[statement 48; assign](){<-}<LSEP>[](symbol){files}<LEND>[call](){}<LSEP>[](symbol){dataDWD}<LSEP>[](symbol){urls}<LEND>[argument 1; call](){}<LSEP>[](symbol){localtestdir}<LEND>[](symbol){F}<LEND>[statement 49; assign](){<-}<LSEP>[](symbol){rv}<LEND>[call](){}<LSEP>[](symbol){readVars}<LSEP>[](symbol){files}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 50; assign](){<-}<LSEP>[](symbol){k}<LEND>[call](){}<LSEP>[](symbol){unlist}<LEND>[argument 0; call](){}<LSEP>[](symbol){lapply}<LSEP>[](symbol){rv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){x}<LSEP>[](symbol){Kurz}<LEND>[statement 51; assign](){<-}<LSEP>[](symbol){nkurzmissing}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){k}<LEND>[statement 52; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){nkurzmissing}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[](symbol){nkurzmissing}<LSEP>[argument 1; litteral](str){/}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){k}<LEND>[argument 3; litteral](str){ DWD abbreviations have no Kur...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){rv_df}<LEND>[call](){}<LSEP>[](symbol){do.call}<LSEP>[](symbol){rbind}<LSEP>[](symbol){rv}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<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; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){rv_df}<LEND>[argument 1; litteral](real){1.000000}<LEND>[litteral](str){Parameter}<LEND>[statement 6; call](){}<LSEP>[](symbol){write.table}<LSEP>[](symbol){rv_df}<LSEP>[argument 1; litteral](str){misc/params.txt}<LSEP>[argument 2; litteral](str){\t}<LSEP>[](symbol){F}<LSEP>[](symbol){F}<LEND>[statement 7; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){- Copy content of 'misc/params...}<LEND>[statement 53; assign](){<-}<LSEP>[](symbol){dupli}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){rv}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){duplicated}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){Kurz}<LEND>[argument 1; litteral](real){0.000000}<LEND>[statement 54; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LSEP>[](symbol){dupli}<LEND>[true branch; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Duplicate Kurz entries in:\n-}<LEND>[argument 1; call](){}<LSEP>[](symbol){truncMessage}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){dupli}<LEND>[](symbol){dupli}<LEND>[argument 1; litteral](str){}<LSEP>[argument 2; litteral](str){\n- }<LSEP>[argument 3; litteral](real){8.000000}<LEND>[statement 55; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){ - To view the checkIndex resu...}<LEND>[statement 56; assign](){<-}<LSEP>[](symbol){a}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){#' # }<LEND>[argument 1; call](){}<LSEP>[](symbol){formatC}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){dwdfiles}<LEND>[argument 1; litteral](str){'}<LEND>[argument 2; litteral](str){ (}<LEND>[argument 3; call](){}<LSEP>[](symbol){Sys.Date}<LEND>[argument 4; litteral](str){)}<LEND>[statement 57; assign](){<-}<LSEP>[](symbol){b}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){#' # }<LEND>[argument 1; call](){}<LSEP>[](symbol){formatC}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){grdfiles}<LEND>[argument 1; litteral](str){'}<LEND>[argument 2; litteral](str){ (}<LEND>[argument 3; call](){}<LSEP>[](symbol){Sys.Date}<LEND>[argument 4; litteral](str){)}<LEND>[statement 58; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){- Manually add these file numb...}<LSEP>[](symbol){a}<LSEP>[argument 2; litteral](str){\n}<LSEP>[](symbol){b}<LEND>[statement 59; assign](){<-}<LSEP>[](symbol){dt}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.time}<LEND>[](symbol){begintime}<LEND>[statement 60; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){Done! updateIndex execution took }<LEND>[argument 1; 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){$}<LSEP>[](symbol){index}<LSEP>[](symbol){checks}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){gl.map.interactive}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){matrix}<LSEP>[](symbol){standard}<LSEP>[](symbol){symmetric}<LSEP>[](symbol){ind.circles}<LSEP>[](symbol){pop.labels}<LSEP>[](symbol){pop.labels.cex}<LSEP>[](symbol){provider}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){pkg}<LSEP>[litteral](str){leaflet}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){requireNamespace}<LSEP>[](symbol){pkg}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Package}<LSEP>[](symbol){pkg}<LSEP>[argument 2; litteral](str){ needed for this function to w...}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){pkg}<LSEP>[litteral](str){leaflet.minicharts}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){requireNamespace}<LSEP>[](symbol){pkg}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Package}<LSEP>[](symbol){pkg}<LSEP>[argument 2; litteral](str){ needed for this function to w...}<LEND>[false branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){genlight}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Not a valid genlight object pr...}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<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){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){latlong}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){centers}<LEND>[call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){df}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){xx}<LEND>[body; call](){}<LSEP>[](symbol){tapply}<LSEP>[](symbol){xx}<LEND>[argument 1; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[](symbol){mean}<LSEP>[argument 3; litteral](logical){TRUE}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){%>%}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){leaflet}<LSEP>[](symbol){leaflet}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){leaflet}<LSEP>[](symbol){addTiles}<LEND>[statement 9; control flow](){if}<LSEP>[](symbol){ind.circles}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){leaflet}<LSEP>[](symbol){addCircleMarkers}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){lon}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){df}<LSEP>[](symbol){lat}<LEND>[argument 2; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cols}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[argument 4; litteral](real){0.800000}<LEND>[statement 10; control flow](){if}<LSEP>[](symbol){pop.labels}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){leaflet}<LSEP>[](symbol){addLabelOnlyMarkers}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){centers}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){lon}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){centers}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){lat}<LEND>[argument 2; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[argument 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){leaflet}<LSEP>[](symbol){labelOptions}<LEND>[](symbol){T}<LSEP>[argument 1; litteral](str){top}<LSEP>[](symbol){T}<LEND>[argument 3; call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){pop.labels.cex}<LSEP>[argument 1; litteral](str){px}<LEND>[statement 11; 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>[](symbol){standard}<LEND>[true branch; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LSEP>[](symbol){}<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){[}<LSEP>[](symbol){matrix}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){matrix}<LSEP>[](symbol){T}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){matrix}<LSEP>[](symbol){T}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){matrix}<LSEP>[](symbol){T}<LEND>[argument 1; litteral](real){9.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; 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; assign](){<-}<LSEP>[](symbol){xys}<LSEP>[](symbol){centers}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){xys}<LSEP>[](symbol){df}<LEND>[statement 2; control flow](){if}<LSEP>[](symbol){symmetric}<LEND>[true branch; 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){nrow}<LSEP>[](symbol){matrix}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){ii}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){matrix}<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){matrix}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){leaflet}<LSEP>[](symbol){addPolylines}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xys}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){lon}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xys}<LSEP>[](symbol){ii}<LSEP>[argument 2; litteral](str){lon}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xys}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](str){lat}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xys}<LSEP>[](symbol){ii}<LSEP>[argument 2; litteral](str){lat}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matrix}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[argument 3; litteral](str){#0000FF}<LSEP>[argument 4; litteral](real){1.000000}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){symmetric}<LEND>[true branch; 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){nrow}<LSEP>[](symbol){matrix}<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){nrow}<LSEP>[](symbol){matrix}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){from}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xys}<LSEP>[](symbol){i}<LSEP>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){to}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xys}<LSEP>[](symbol){ii}<LSEP>[](symbol){}<LEND>[statement 2; 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){[}<LSEP>[](symbol){matrix}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matrix}<LSEP>[](symbol){ii}<LSEP>[](symbol){i}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matrix}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matrix}<LSEP>[](symbol){ii}<LSEP>[](symbol){i}<LEND>[true branch; assign](){=}<LSEP>[](symbol){lcols}<LSEP>[litteral](str){#FFAA00}<LEND>[false branch; assign](){=}<LSEP>[](symbol){lcols}<LSEP>[litteral](str){#00AAFF}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matrix}<LSEP>[](symbol){i}<LSEP>[](symbol){ii}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){matrix}<LSEP>[](symbol){ii}<LSEP>[](symbol){i}<LEND>[true branch; assign](){=}<LSEP>[](symbol){lcols}<LSEP>[litteral](str){#00AA00}<LEND>[false branch; assign](){=}<LSEP>[](symbol){lcols}<LSEP>[litteral](str){#333333}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){m}<LEND>[call](){}<LSEP>[](symbol){%>%}<LSEP>[](symbol){m}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){leaflet.minicharts}<LSEP>[](symbol){addFlows}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){from}<LSEP>[argument 1; litteral](str){lon}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; 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}
[](){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; litteral](str){SCALE}<LEND>[](symbol){scal}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){Every class indicated by sibli...}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){x.original}<LSEP>[](symbol){x}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){exist.orderparent}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){Order}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){parent.class}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){exist.orderclass}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){Order}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){exist.ordersibling}<LEND>[call](){}<LSEP>[](symbol){logical}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){sibling.classes}<LEND>[statement 12; control flow](){for}<LSEP>[](symbol){cl}<LSEP>[](symbol){sibling.classes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exist.ordersibling}<LSEP>[](symbol){cl}<LEND>[call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){Order}<LEND>[argument 1; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){cl}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){exist.orderparent}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){mtgorder}<LSEP>[](symbol){x}<LSEP>[](symbol){parent.class}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){exist.orderclass}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){mtgorder}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[statement 15; control flow](){for}<LSEP>[](symbol){cl}<LSEP>[](symbol){sibling.classes}<LEND>[body; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){exist.ordersibling}<LSEP>[](symbol){cl}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){mtgorder}<LSEP>[](symbol){x}<LSEP>[](symbol){cl}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){tabclass}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){tabparent}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){parent.class}<LEND>[statement 18; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){sibling.classes}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){tabsibl}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){sibling.classes}<LEND>[statement 19; assign](){<-}<LSEP>[](symbol){v.class}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tabclass}<LSEP>[argument 1; litteral](str){Order}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){v.class}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){v.class}<LEND>[argument 1; call](){}<LSEP>[](symbol){character}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){v.class}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){v.parent}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){tabparent}<LSEP>[argument 1; litteral](str){Order}<LEND>[statement 22; 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; assign](){<-}<LSEP>[](symbol){v.sibling}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){numeric}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; control flow](){for}<LSEP>[](symbol){cl}<LSEP>[](symbol){sibling.classes}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){v.sibling}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){v.sibling}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){tabsibl}<LSEP>[](symbol){cl}<LEND>[argument 1; litteral](str){Order}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){v.sibling}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){v.sibling}<LEND>[argument 1; call](){}<LSEP>[](symbol){character}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){v.sibling}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){v.class}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.class}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){v.class}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){v.parent}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.parent}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){v.parent}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){sibling.classes}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){v.sibling}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.sibling}<LEND>[argument 1; call](){}<LSEP>[](symbol){sort}<LEND>[argument 0; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){v.sibling}<LEND>[](symbol){}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[statement 26; control flow](){for}<LSEP>[](symbol){v}<LEND>[range; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){v.class}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ord}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.class}<LSEP>[](symbol){v}<LSEP>[argument 2; litteral](str){Order}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i.parent}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.parent}<LSEP>[](symbol){Order}<LEND>[](symbol){ord}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){v.parent}<LEND>[](symbol){v}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.class}<LSEP>[](symbol){v}<LSEP>[argument 2; litteral](str){parent}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){v.parent}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){i.parent}<LEND>[statement 27; 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](){for}<LSEP>[](symbol){v}<LEND>[range; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){v.sibling}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ord}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.sibling}<LSEP>[](symbol){v}<LSEP>[argument 2; litteral](str){Order}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){i.parent}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.parent}<LSEP>[](symbol){Order}<LEND>[](symbol){ord}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){v.parent}<LEND>[](symbol){v}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.sibling}<LSEP>[](symbol){v}<LSEP>[argument 2; litteral](str){parent}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){v.parent}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){i.parent}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){method}<LEND>[call](){}<LSEP>[](symbol){substring}<LSEP>[](symbol){from}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[statement 29; control flow](){if}<LSEP>[](symbol){relative}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){method}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){r}<LEND>[false branch; assign](){<-}<LSEP>[](symbol){method}<LEND>[call](){}<LSEP>[](symbol){paste0}<LSEP>[](symbol){method}<LSEP>[argument 1; litteral](str){a}<LEND>[statement 30; assign](){<-}<LSEP>[](symbol){v.ranks}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[argument 0; litteral](str){classe}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.class}<LSEP>[argument 1; litteral](str){parent}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 31; 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; assign](){<-}<LSEP>[](symbol){v.ranks}<LEND>[call](){}<LSEP>[](symbol){rbind}<LSEP>[](symbol){v.ranks}<LEND>[argument 1; call](){}<LSEP>[](symbol){data.frame}<LSEP>[argument 0; litteral](str){sibling}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.sibling}<LSEP>[argument 1; litteral](str){parent}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[statement 32; assign](){<-}<LSEP>[](symbol){v.ranks}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){v.ranks}<LEND>[argument 1; call](){}<LSEP>[](symbol){numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){v.ranks}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 33; assign](){<-}<LSEP>[](symbol){v.ranks}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.ranks}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[argument 1; call](){}<LSEP>[](symbol){row.names}<LSEP>[](symbol){v.ranks}<LEND>[](symbol){}<LEND>[statement 34; call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){method}<LEND>[argument 1; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){vpa}<LEND>[range; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.ranks}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[](symbol){vpa}<LEND>[argument 2; litteral](str){Rank}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[](symbol){vpa}<LEND>[argument 2; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){vpa}<LEND>[range; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ranks}<LEND>[call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[](symbol){vpa}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.ranks}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[](symbol){vpa}<LEND>[argument 2; litteral](str){Rank}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ranks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){ranks}<LEND>[argument 3; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){vpa}<LEND>[range; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.ranks}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[](symbol){vpa}<LEND>[argument 2; litteral](str){Rank}<LEND>[call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[](symbol){vpa}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 4; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){vpa}<LEND>[range; call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ranks}<LEND>[call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[](symbol){vpa}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.ranks}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){v.ranks}<LSEP>[](symbol){parent}<LEND>[](symbol){vpa}<LEND>[argument 2; litteral](str){Rank}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){ranks}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){ranks}<LEND>[](symbol){}<LEND>[statement 35; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){v.ranks}<LEND>[argument 1; call](){}<LSEP>[](symbol){row.names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[argument 2; litteral](str){Rank}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 36; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){rank.name}<LSEP>[argument 1; litteral](str){Rank}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){j.rank}<LEND>[call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[argument 1; litteral](str){Rank}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[](symbol){j.rank}<LEND>[](symbol){rank.name}<LEND>[statement 37; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){union}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x.original}<LSEP>[](symbol){classe}<LEND>[argument 1; litteral](str){Rank}<LEND>[statement 38; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[](symbol){parent.class}<LEND>[call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x.original}<LSEP>[](symbol){parent.class}<LEND>[statement 39; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){sibling.classes}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x.original}<LSEP>[](symbol){sibling.classes}<LEND>[statement 40; control flow](){if}<LSEP>[](symbol){display}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){\t}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[argument 0; litteral](str){absolute}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){relative}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[argument 0; litteral](str){relative}<LSEP>[](symbol){relative}<LEND>[argument 3; litteral](str){ranks: from the}<LSEP>[](symbol){from}<LSEP>[argument 5; litteral](str){\n\n}<LEND>[statement 1; call](){}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){classe}<LEND>[statement 41; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){invisible}<LSEP>[](symbol){x}
[](){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; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[](symbol){cutcol}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){cutcol: some column numbers ar...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){notnum}<LEND>[call](){}<LSEP>[](symbol){setdiff}<LSEP>[](symbol){cutcol}<LSEP>[](symbol){colnum}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){notnum}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){warning}<LSEP>[argument 0; litteral](str){Non-numeric columns cannot be ...}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cutcol}<LEND>[call](){}<LSEP>[](symbol){intersect}<LSEP>[](symbol){cutcol}<LSEP>[](symbol){colnum}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cutcol}<LSEP>[](symbol){colnum}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){breaks}<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){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){labels}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){labels}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){If breaks is a list, labels mu...}<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){is.null}<LSEP>[](symbol){cutcol}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){breaks}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cutcol}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){If breaks is a list, its lengt...}<LEND>[statement 2; 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.null}<LSEP>[](symbol){labels}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){labels}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){cutcol}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){If labels is a list, its lengt...}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){all}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){breaks}<LSEP>[](symbol){cutcol}<LEND>[](symbol){is.numeric}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){breaks must be either numeric ...}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){nbr}<LEND>[call](){}<LSEP>[](symbol){sapply}<LSEP>[](symbol){breaks}<LSEP>[](symbol){length}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){nbr}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){any}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LSEP>[](symbol){nbr}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){invalid number of intervals}<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){breaks}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){breaks must be either numeric ...}<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){is.null}<LSEP>[](symbol){labels}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LSEP>[](symbol){labels}<LEND>[true branch; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){labels: wrong value.}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){brk}<LSEP>[](symbol){breaks}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){breaks}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){breaks}<LSEP>[](symbol){j}<LEND>[](symbol){brk}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LSEP>[](symbol){labels}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){lab}<LSEP>[](symbol){labels}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){labels}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 2; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){p}<LEND>[body; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){labels}<LSEP>[](symbol){j}<LEND>[](symbol){lab}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){j}<LSEP>[](symbol){cutcol}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){cut}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[](symbol){j}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){breaks}<LSEP>[](symbol){j}<LEND>[argument 2; litteral](logical){TRUE}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){x}
[](){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}
[](){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}
[](){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; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){lon}<LSEP>[argument 1; litteral](str){lat}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){xy}<LEND>[true branch; call](){}<LSEP>[](symbol){step}<LSEP>[argument 0; litteral](str){No coordinates found in the ge...}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dist.type}<LSEP>[argument 1; litteral](str){pop}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){c.x}<LEND>[call](){}<LSEP>[](symbol){tapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){xy}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){pop}<LEND>[](symbol){mean}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){c.y}<LEND>[call](){}<LSEP>[](symbol){tapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){xy}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){pop}<LEND>[](symbol){mean}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){cp}<LEND>[call](){}<LSEP>[](symbol){cbind}<LSEP>[](symbol){c.x}<LSEP>[](symbol){c.y}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){eucl.mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){dist}<LSEP>[](symbol){cp}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){eucl.mat}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){popNames}<LSEP>[](symbol){x}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){npop}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){levels}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){pop}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cp}<LEND>[call](){}<LSEP>[](symbol){cbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){xy}<LEND>[](symbol){}<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){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){xy}<LEND>[](symbol){}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){eucl.mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){dist}<LSEP>[](symbol){cp}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){eucl.mat}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){npop}<LEND>[call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){indNames}<LSEP>[](symbol){x}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){mats}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){mats.names}<LSEP>[litteral](logical){NA}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){mats.pathlength}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){mats.paths}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){pathlength.mat}<LSEP>[litteral](NULL){NULL}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){paths}<LSEP>[litteral](NULL){NULL}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){n.mats}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){fric.raster}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 18; control flow](){for}<LSEP>[](symbol){ci}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n.mats}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){raster}<LSEP>[](symbol){plot}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fric.raster}<LSEP>[](symbol){ci}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fric.raster}<LEND>[](symbol){ci}<LEND>[argument 1; litteral](str){:}<LSEP>[](symbol){pathtype}<LSEP>[argument 3; litteral](str){, NN=}<LSEP>[](symbol){NN}<LSEP>[argument 5; litteral](str){}<LEND>[statement 1; call](){}<LSEP>[](symbol){points}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){x}<LSEP>[](symbol){other}<LEND>[](symbol){xy}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){16.000000}<LEND>[argument 3; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){rainbow}<LEND>[argument 0; call](){}<LSEP>[](symbol){nPop}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){as.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){pop}<LSEP>[](symbol){x}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dist.type}<LSEP>[argument 1; litteral](str){pop}<LEND>[true branch; call](){}<LSEP>[](symbol){points}<LSEP>[](symbol){cp}<LSEP>[argument 1; litteral](real){1.500000}<LSEP>[argument 2; litteral](real){15.000000}<LSEP>[argument 3; litteral](str){black}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){fric.mat}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){gdistance}<LSEP>[](symbol){transition}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){fric.raster}<LSEP>[](symbol){ci}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){NN}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){@}<LEND>[argument 0; call](){}<LSEP>[](symbol){@}<LSEP>[](symbol){fric.mat}<LSEP>[](symbol){crs}<LEND>[](symbol){projargs}<LEND>[litteral](str){+proj=merc +units=m}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){fric.mat.cor}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){gdistance}<LSEP>[](symbol){geoCorrection}<LEND>[](symbol){fric.mat}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){pathtype}<LSEP>[argument 1; litteral](str){leastcost}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){cd.mat}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){gdistance}<LSEP>[](symbol){costDistance}<LEND>[](symbol){fric.mat.cor}<LSEP>[](symbol){cp}<LSEP>[](symbol){cp}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){pathtype}<LSEP>[argument 1; litteral](str){rSPDistance}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){cd.mat}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){gdistance}<LSEP>[](symbol){rSPDistance}<LEND>[](symbol){fric.mat.cor}<LSEP>[](symbol){cp}<LSEP>[](symbol){cp}<LSEP>[argument 3; litteral](real){1.000000}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){pathtype}<LSEP>[argument 1; litteral](str){commute}<LEND>[true branch; assign](){<-}<LSEP>[](symbol){cd.mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){gdistance}<LSEP>[](symbol){commuteDistance}<LEND>[](symbol){fric.mat.cor}<LSEP>[](symbol){cp}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){cd.mat}<LEND>[call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){eucl.mat}<LEND>[statement 10; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){pathtype}<LSEP>[argument 1; litteral](str){leastcost}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){plotpath}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){comb}<LEND>[call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){combn}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){npop}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){pathlength.mat}<LSEP>[](symbol){cd.mat}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pathlength.mat}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[litteral](real){0.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){paths}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){cols}<LEND>[call](){}<LSEP>[](symbol){rainbow}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){comb}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.500000}<LEND>[statement 5; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){comb}<LEND>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){dist}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comb}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comb}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ll}<LEND>[call](){}<LSEP>[](symbol){Line}<LEND>[argument 0; call](){}<LSEP>[](symbol){rbind}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comb}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comb}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){S1}<LEND>[call](){}<LSEP>[](symbol){Lines}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){ll}<LEND>[argument 1; litteral](str){Null}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){sPath}<LEND>[call](){}<LSEP>[](symbol){SpatialLines}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){S1}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sPath}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){gdistance}<LSEP>[](symbol){shortestPath}<LEND>[](symbol){fric.mat.cor}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comb}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cp}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comb}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[argument 3; litteral](str){SpatialLines}<LEND>[statement 1; call](){}<LSEP>[](symbol){lines}<LSEP>[](symbol){sPath}<LSEP>[argument 1; litteral](real){1.500000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){cols}<LSEP>[](symbol){i}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){paths}<LSEP>[](symbol){i}<LEND>[](symbol){sPath}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){ll}<LEND>[call](){}<LSEP>[](symbol){round}<LEND>[argument 0; call](){}<LSEP>[](symbol){SpatialLinesLengths}<LSEP>[](symbol){sPath}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pathlength.mat}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comb}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comb}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[](symbol){ll}<LEND>[statement 5; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pathlength.mat}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comb}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){2.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){comb}<LSEP>[](symbol){i}<LSEP>[argument 2; litteral](real){1.000000}<LEND>[](symbol){ll}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){mats}<LSEP>[](symbol){ci}<LEND>[](symbol){cd.mat}<LEND>[statement 12; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){mats.names}<LSEP>[](symbol){ci}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fric.raster}<LEND>[](symbol){ci}<LEND>[statement 13; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){mats.pathlength}<LSEP>[](symbol){ci}<LEND>[](symbol){pathlength.mat}<LEND>[statement 14; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){mats.paths}<LSEP>[](symbol){ci}<LEND>[](symbol){paths}<LEND>[statement 19; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){mats}<LEND>[call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){fric.raster}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){xx}<LEND>[call](){}<LSEP>[](symbol){gl2gi}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 21; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){Gst.Nei}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gendist.mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){mmod}<LSEP>[](symbol){pairwise_Gst_Nei}<LEND>[](symbol){xx}<LEND>[statement 22; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){Gst.Hedrick}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gendist.mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){mmod}<LSEP>[](symbol){pairwise_Gst_Hedrick}<LEND>[](symbol){xx}<LEND>[statement 23; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){D}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gendist.mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){mmod}<LSEP>[](symbol){pairwise_D}<LEND>[](symbol){xx}<LEND>[statement 24; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){Smouse}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gendist.mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){gd.smouse}<LSEP>[](symbol){xx}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 25; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){Kosman}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gendist.mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.dist}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){gd.kosman}<LSEP>[](symbol){xx}<LEND>[](symbol){geneticdist}<LEND>[statement 26; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){gen.distance}<LSEP>[argument 1; litteral](str){propShared}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){gendist.mat}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.dist}<LEND>[argument 0; call](){}<LSEP>[](symbol){propShared}<LSEP>[](symbol){xx}<LEND>[statement 27; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){gendist.mat}<LEND>[call](){}<LSEP>[](symbol){dimnames}<LSEP>[](symbol){eucl.mat}<LEND>[statement 28; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){gendist.mat}<LSEP>[](symbol){eucl.mat}<LSEP>[](symbol){mats.names}<LSEP>[](symbol){mats}<LSEP>[](symbol){mats.pathlength}<LSEP>[](symbol){mats.paths}
[](){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}
[](){expression}<LSEP>[litteral](str){possums.gl}<LSEP>[litteral](str){bandicoot.gl}<LSEP>[litteral](str){testset.gl}<LSEP>[litteral](str){testset.gs}<LSEP>[litteral](NULL){NULL}<LSEP>[litteral](NULL){NULL}<LSEP>[litteral](NULL){NULL}<LSEP>[litteral](NULL){NULL}
[](){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}
[](){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}
[](){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}
[](){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}
[](){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}
[](){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}
[](){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}
[](){expression}<LSEP>[litteral](NULL){NULL}
[](){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}
[](){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}
[](){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}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){cramer.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){xf}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){xf}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){group}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){group}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){by}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LSEP>[](symbol){cramer.data.frame}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[assign](){<-}<LSEP>[](symbol){tschuprow.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){xf}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){xf}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){group}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){group}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){by}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LSEP>[](symbol){cramer.data.frame}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[assign](){<-}<LSEP>[](symbol){pearson.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){xf}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){xf}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){group}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){group}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){by}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LSEP>[](symbol){pearson.data.frame}<LSEP>[argument 3; litteral](logical){FALSE}<LEND>[assign](){<-}<LSEP>[](symbol){phi.folder}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){xf}<LEND>[body; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LSEP>[](symbol){xf}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; assign](){=}<LSEP>[](symbol){group}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](str){group}<LEND>[statement 2; assign](){=}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){x}<LEND>[statement 3; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){by}<LSEP>[](symbol){x}<LSEP>[](symbol){group}<LSEP>[](symbol){pearson.data.frame}<LSEP>[argument 3; litteral](logical){FALSE}
[](){expression}<LSEP>[assign](){<-}<LSEP>[variable; litteral](str){dtt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){type}<LSEP>[](symbol){variant}<LSEP>[](symbol){inverted}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){dtt}<LSEP>[](symbol){type}<LSEP>[](symbol){variant}<LSEP>[](symbol){inverted}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.data.frame}<LSEP>[](symbol){x}<LEND>[true branch; call](){}<LSEP>[](symbol){t}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){dtt}<LSEP>[](symbol){type}<LSEP>[](symbol){variant}<LSEP>[](symbol){inverted}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){res}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){type}<LEND>[call](){}<LSEP>[](symbol){match.arg}<LSEP>[](symbol){type}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){transform}<LEND>[call](){}<LSEP>[](symbol){switch}<LSEP>[](symbol){type}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){2.000000}<LSEP>[argument 3; litteral](real){3.000000}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){transform}<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){==}<LSEP>[](symbol){variant}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){0.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; 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){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<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){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){cos}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){k}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<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){==}<LSEP>[](symbol){variant}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){inverted}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){variant}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){cos}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[](symbol){n}<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>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.500000}<LEND>[](symbol){k}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n}<LEND>[statement 2; 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){variant}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){inverted}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){variant}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){0.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){cos}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){variant}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){cos}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[](symbol){n}<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>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){transform}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){variant}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sin}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){n}<LSEP>[argument 1; 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>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<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){==}<LSEP>[](symbol){variant}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){inverted}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){variant}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sin}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[](symbol){n}<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>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n}<LEND>[statement 2; 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){variant}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){inverted}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){&&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){variant}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<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>[](symbol){k}<LEND>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<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){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){sin}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[](symbol){n}<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>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){variant}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sin}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){pi}<LSEP>[](symbol){n}<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>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.500000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){0.500000}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){n}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){transform}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){for}<LSEP>[](symbol){k}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){k}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){cos}<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){2.000000}<LSEP>[](symbol){pi}<LEND>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){k}<LEND>[argument 1; call](){}<LSEP>[](symbol){sin}<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){2.000000}<LSEP>[](symbol){pi}<LEND>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){n}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](symbol){k}<LEND>[statement 1; control flow](){if}<LSEP>[](symbol){inverted}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){=}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[statement 5; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){DWT.TRANSFORM.TYPE}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[assign](){<-}<LSEP>[](symbol){UDWT.TRANSFORM.TYPE}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){MAD.VARIANCE.ESTIMATOR}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[assign](){<-}<LSEP>[](symbol){STD.VARIANCE.ESTIMATOR}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){SOFT.THRESHOLD.TYPE}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[assign](){<-}<LSEP>[](symbol){HARD.THRESHOLD.TYPE}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[assign](){<-}<LSEP>[](symbol){MAX.DECOMPOSITION}<LSEP>[litteral](real){0.000000}<LEND>[assign](){<-}<LSEP>[](symbol){CALC.THRESHOLD.TO.USE}<LSEP>[litteral](real){0.000000}<LEND>[assign](){<-}<LSEP>[](symbol){DEFAULT.DWT.THRESHOLD.MULTIPLIER}<LSEP>[litteral](real){3.000000}<LEND>[assign](){<-}<LSEP>[](symbol){DEFAULT.UDWT.THRESHOLD.MULTIPLIER}<LSEP>[litteral](real){3.600000}<LEND>[assign](){<-}<LSEP>[](symbol){default.dwt.option}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](logical){FALSE}<LSEP>[](symbol){DEFAULT.DWT.THRESHOLD.MULTIPLIER}<LSEP>[](symbol){MAD.VARIANCE.ESTIMATOR}<LSEP>[](symbol){SOFT.THRESHOLD.TYPE}<LSEP>[](symbol){MAX.DECOMPOSITION}<LSEP>[](symbol){CALC.THRESHOLD.TO.USE}<LEND>[assign](){<-}<LSEP>[](symbol){default.udwt.option}<LEND>[call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](logical){FALSE}<LSEP>[](symbol){DEFAULT.UDWT.THRESHOLD.MULTIPLIER}<LSEP>[](symbol){MAD.VARIANCE.ESTIMATOR}<LSEP>[](symbol){HARD.THRESHOLD.TYPE}<LSEP>[](symbol){MAX.DECOMPOSITION}<LSEP>[](symbol){CALC.THRESHOLD.TO.USE}<LEND>[assign](){<-}<LSEP>[](symbol){denoise}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){type}<LSEP>[](symbol){option}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){start denoising via wavelet tr...}<LEND>[statement 1; call](){}<LSEP>[](symbol){.validate.denoise.args}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){type}<LSEP>[](symbol){option}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){res}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[](symbol){DWT.TRANSFORM.TYPE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){.dwt}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){option}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){.udwt}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){option}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){option}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[](symbol){option}<LSEP>[](symbol){type}<LEND>[statement 4; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){res}<LSEP>[](symbol){thld}<LEND>[statement 5; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){end denoising via wavelet tran...}<LEND>[statement 6; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){res}<LSEP>[](symbol){xd}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){res}<LSEP>[](symbol){xd}<LEND>[](symbol){option}<LEND>[assign](){<-}<LSEP>[](symbol){denoise.dwt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){option}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){start decimated wavelet transform}<LEND>[statement 1; call](){}<LSEP>[](symbol){denoise}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){DWT.TRANSFORM.TYPE}<LSEP>[](symbol){option}<LEND>[assign](){<-}<LSEP>[](symbol){denoise.udwt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){option}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){message}<LSEP>[argument 0; litteral](str){start undecimated wavelet tran...}<LEND>[statement 1; call](){}<LSEP>[](symbol){denoise}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){UDWT.TRANSFORM.TYPE}<LSEP>[](symbol){option}<LEND>[assign](){<-}<LSEP>[](symbol){.dwt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){option}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){initValues}<LEND>[call](){}<LSEP>[](symbol){.init.denoise}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){num.decompression.levels}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mx}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){initValues}<LSEP>[](symbol){mx}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nx}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){initValues}<LSEP>[](symbol){nx}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dimen}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){initValues}<LSEP>[](symbol){dimen}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){initValues}<LSEP>[](symbol){n}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){L}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){initValues}<LSEP>[](symbol){L}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){ret.mdwt}<LEND>[call](){}<LSEP>[](symbol){mdwt}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){L}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){xd}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ret.mdwt}<LSEP>[](symbol){y}<LEND>[statement 8; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){ret.mdwt}<LEND>[statement 9; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold}<LEND>[](symbol){CALC.THRESHOLD.TO.USE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xd}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){mx}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){mx}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){nx}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){nx}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){variance.estimator}<LEND>[](symbol){MAD.VARIANCE.ESTIMATOR}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){thld}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.multiplier}<LEND>[argument 1; call](){}<LSEP>[](symbol){median}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](real){0.670000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){variance.estimator}<LEND>[](symbol){STD.VARIANCE.ESTIMATOR}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){thld}<LEND>[call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.multiplier}<LEND>[argument 1; call](){}<LSEP>[](symbol){std}<LSEP>[](symbol){tmp}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){unknown variance estimator - u...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){thld}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold}<LEND>[statement 10; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){thld =}<LSEP>[](symbol){thld}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dimen}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ix}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){L}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){ykeep}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xd}<LSEP>[](symbol){ix}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){ix}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){mx}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){L}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){jx}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){nx}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){L}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){ykeep}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xd}<LSEP>[](symbol){ix}<LSEP>[](symbol){jx}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.type}<LEND>[](symbol){SOFT.THRESHOLD.TYPE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xd}<LEND>[call](){}<LSEP>[](symbol){softTh}<LSEP>[](symbol){xd}<LSEP>[](symbol){thld}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.type}<LEND>[](symbol){HARD.THRESHOLD.TYPE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xd}<LEND>[call](){}<LSEP>[](symbol){hardTh}<LSEP>[](symbol){xd}<LSEP>[](symbol){thld}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){unknown threshold type - use e...}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.low.pass.part}<LEND>[argument 1; litteral](logical){FALSE}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dimen}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xd}<LSEP>[](symbol){ix}<LEND>[](symbol){ykeep}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xd}<LSEP>[](symbol){ix}<LSEP>[](symbol){jx}<LEND>[](symbol){ykeep}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){ret.midwt}<LEND>[call](){}<LSEP>[](symbol){midwt}<LSEP>[](symbol){xd}<LSEP>[](symbol){h}<LSEP>[](symbol){L}<LEND>[statement 15; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ret.midwt}<LSEP>[](symbol){x}<LEND>[](symbol){thld}<LEND>[assign](){<-}<LSEP>[](symbol){.udwt}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){option}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){initValues}<LEND>[call](){}<LSEP>[](symbol){.init.denoise}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){num.decompression.levels}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){mx}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){initValues}<LSEP>[](symbol){mx}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){nx}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){initValues}<LSEP>[](symbol){nx}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){dimen}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){initValues}<LSEP>[](symbol){dimen}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){initValues}<LSEP>[](symbol){n}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){L}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){initValues}<LSEP>[](symbol){L}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){ret.mrdwt}<LEND>[call](){}<LSEP>[](symbol){mrdwt}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){L}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){xl}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ret.mrdwt}<LSEP>[](symbol){yl}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){xh}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ret.mrdwt}<LSEP>[](symbol){yh}<LEND>[statement 9; call](){}<LSEP>[](symbol){rm}<LSEP>[](symbol){ret.mrdwt}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){c.offset}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dimen}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; litteral](real){1.000000}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){nx}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 11; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold}<LEND>[](symbol){CALC.THRESHOLD.TO.USE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){tmp}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){xh}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){c.offset}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){c.offset}<LSEP>[](symbol){nx}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){variance.estimator}<LEND>[](symbol){MAD.VARIANCE.ESTIMATOR}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){thld}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.multiplier}<LEND>[argument 1; call](){}<LSEP>[](symbol){median}<LEND>[argument 0; call](){}<LSEP>[](symbol){abs}<LSEP>[](symbol){tmp}<LEND>[argument 1; litteral](real){0.670000}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){variance.estimator}<LEND>[](symbol){STD.VARIANCE.ESTIMATOR}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){thld}<LEND>[call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.multiplier}<LEND>[argument 1; call](){}<LSEP>[](symbol){std}<LSEP>[](symbol){tmp}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){unknown variance estimator - u...}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){thld}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold}<LEND>[statement 12; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){thld =}<LSEP>[](symbol){thld}<LSEP>[argument 2; litteral](str){\n}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.type}<LEND>[](symbol){SOFT.THRESHOLD.TYPE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xh}<LEND>[call](){}<LSEP>[](symbol){softTh}<LSEP>[](symbol){xh}<LSEP>[](symbol){thld}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.low.pass.part}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xl}<LEND>[call](){}<LSEP>[](symbol){softTh}<LSEP>[](symbol){xl}<LSEP>[](symbol){thld}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.type}<LEND>[](symbol){HARD.THRESHOLD.TYPE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xh}<LEND>[call](){}<LSEP>[](symbol){hardTh}<LSEP>[](symbol){xh}<LSEP>[](symbol){thld}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.low.pass.part}<LEND>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){xl}<LEND>[call](){}<LSEP>[](symbol){hardTh}<LSEP>[](symbol){xl}<LSEP>[](symbol){thld}<LEND>[false branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){unknown threshold type - use e...}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){ret.mirdwt}<LEND>[call](){}<LSEP>[](symbol){mirdwt}<LSEP>[](symbol){xl}<LSEP>[](symbol){xh}<LSEP>[](symbol){h}<LSEP>[](symbol){L}<LEND>[statement 15; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){ret.mirdwt}<LSEP>[](symbol){x}<LEND>[](symbol){thld}<LEND>[assign](){<-}<LSEP>[](symbol){.init.denoise}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){num.levels}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){mx}<LEND>[call](){}<LSEP>[](symbol){nrow}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){nx}<LEND>[call](){}<LSEP>[](symbol){ncol}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.matrix}<LSEP>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){dimen}<LEND>[call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){mx}<LSEP>[](symbol){nx}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){n}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){dimen}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){max}<LSEP>[](symbol){mx}<LSEP>[](symbol){nx}<LEND>[false branch; block](){}<LSEP>[](symbol){dimen}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){L}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){num.levels}<LSEP>[](symbol){MAX.DECOMPOSITION}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){floor}<LEND>[argument 0; call](){}<LSEP>[](symbol){log2}<LSEP>[](symbol){n}<LEND>[false branch; block](){}<LSEP>[](symbol){num.levels}<LEND>[statement 5; call](){}<LSEP>[](symbol){list}<LSEP>[](symbol){mx}<LSEP>[](symbol){nx}<LSEP>[](symbol){dimen}<LSEP>[](symbol){n}<LSEP>[](symbol){L}<LEND>[assign](){<-}<LSEP>[](symbol){.validate.denoise.args}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){h}<LSEP>[](symbol){type}<LSEP>[](symbol){option}<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.vector}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){is.matrix}<LSEP>[](symbol){x}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){argument %s must be vector or ...}<LEND>[argument 1; call](){}<LSEP>[](symbol){sQuote}<LSEP>[argument 0; litteral](str){x}<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){is.vector}<LSEP>[](symbol){h}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){h}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){argument %s must be vector con...}<LEND>[argument 1; call](){}<LSEP>[](symbol){sQuote}<LSEP>[argument 0; litteral](str){h}<LEND>[statement 2; 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){type}<LSEP>[](symbol){DWT.TRANSFORM.TYPE}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){type}<LSEP>[](symbol){UDWT.TRANSFORM.TYPE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){argument %s specifies unknown ...}<LEND>[argument 1; call](){}<LSEP>[](symbol){sQuote}<LSEP>[argument 0; litteral](str){type}<LEND>[statement 3; 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.list}<LSEP>[](symbol){option}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){option}<LEND>[argument 1; litteral](real){6.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){argument %s must be list conta...}<LEND>[argument 1; call](){}<LSEP>[](symbol){sQuote}<LSEP>[argument 0; litteral](str){option}<LEND>[statement 4; call](){}<LSEP>[](symbol){.validate.denoise.option.args}<LSEP>[](symbol){option}<LEND>[assign](){<-}<LSEP>[](symbol){.validate.denoise.option.args}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){option}<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){is.logical}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.low.pass.part}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){argument %s must be logical}<LEND>[argument 1; call](){}<LSEP>[](symbol){sQuote}<LSEP>[argument 0; litteral](str){option[[1]]}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.multiplier}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){argument %s must be numeric}<LEND>[argument 1; call](){}<LSEP>[](symbol){sQuote}<LSEP>[argument 0; litteral](str){option[[2]]}<LEND>[statement 2; 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){$}<LSEP>[](symbol){option}<LSEP>[](symbol){variance.estimator}<LEND>[](symbol){MAD.VARIANCE.ESTIMATOR}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){variance.estimator}<LEND>[](symbol){STD.VARIANCE.ESTIMATOR}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){argument %s must be 0 or 1}<LEND>[argument 1; call](){}<LSEP>[](symbol){sQuote}<LSEP>[argument 0; litteral](str){option[[3]]}<LEND>[statement 3; 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){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.type}<LEND>[](symbol){SOFT.THRESHOLD.TYPE}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold.type}<LEND>[](symbol){HARD.THRESHOLD.TYPE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){argument %s must be 0 or 1}<LEND>[argument 1; call](){}<LSEP>[](symbol){sQuote}<LSEP>[argument 0; litteral](str){option[[4]]}<LEND>[statement 4; 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){as.integer}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){num.decompression.levels}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){argument %s must be natural nu...}<LEND>[argument 1; call](){}<LSEP>[](symbol){sQuote}<LSEP>[argument 0; litteral](str){option[[5]]}<LEND>[statement 5; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.numeric}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){option}<LSEP>[](symbol){threshold}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){argument %s must be numeric ve...}<LEND>[argument 1; call](){}<LSEP>[](symbol){sQuote}<LSEP>[argument 0; litteral](str){option[[6]]}
[](){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; call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){3.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){4.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){5.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){6.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){7.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){8.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){9.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){b2n}<LSEP>[argument 0; litteral](real){11.000000}<LEND>[argument 1; 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; litteral](real){1.000000}<LEND>[statement 5; 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){16.000000}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){clutter}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.integer}<LSEP>[](symbol){val}
[](){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}