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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){pqr2Ps}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){p}<LSEP>[](symbol){q}<LSEP>[](symbol){r}<LSEP>[](symbol){useExact}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[](symbol){useExact}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){res}<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){p}<LSEP>[](symbol){q}<LEND>[](symbol){r}<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){*}<LSEP>[argument 0; litteral](real){4.000000}<LSEP>[](symbol){p}<LEND>[](symbol){q}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){perfectParsCharTree}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){tree}<LSEP>[](symbol){nchar}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){inherits}<LSEP>[](symbol){tree}<LSEP>[argument 1; litteral](str){phylo}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){tree must be of class 'phylo'}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){charMat}<LEND>[call](){}<LSEP>[](symbol){matrix}<LSEP>[argument 0; litteral](real){0.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){Ntip}<LSEP>[](symbol){tree}<LEND>[](symbol){nchar}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){rownames}<LSEP>[](symbol){charMat}<LEND>[call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){tree}<LSEP>[](symbol){tip.label}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){desc}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){sampleRanges}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){r}<LSEP>[](symbol){alpha}<LSEP>[](symbol){beta}<LSEP>[](symbol){rTimeRatio}<LSEP>[](symbol){modern.samp.prob}<LSEP>[](symbol){min.taxa}<LSEP>[](symbol){ranges.only}<LSEP>[](symbol){minInt}<LSEP>[](symbol){merge.cryptic}<LSEP>[](symbol){randLiveHat}<LSEP>[](symbol){alt.method}<LSEP>[](symbol){plot}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){taxaData}<LEND>[argument 1; litteral](real){6.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){living}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){taxaData}<LSEP>[](symbol){}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cryptic}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; 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