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add an additional method to genus.to.species.tree #5

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add an additional method to genus.to.species.tree #5

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14 changes: 9 additions & 5 deletions R/add.species.to.genus.R
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Expand Up @@ -40,18 +40,22 @@ add.species.to.genus<-function(tree,species,genus=NULL,where=c("root","random"))
## function take genus backbone tree & converts genus tree to species tree by simulating pure-birth subtrees
## written by Liam J. Revell 2015

genus.to.species.tree<-function(tree,species){
genus.to.species.tree<-function(tree,species, method = c("random", "star")){
N<-Ntip(tree)
genera<-tree$tip.label
species<-gsub(" ","_",species)
method <- method[1]
for(i in 1:N){
jj<-grep(paste(genera[i],"_",sep=""),species)
nn<-which(tree$tip.label==genera[i])
if(length(jj)>1){
h<-runif(n=1)*tree$edge.length[which(tree$edge[,2]==nn)]
tree$edge.length[which(tree$edge[,2]==nn)]<-
tree$edge.length[which(tree$edge[,2]==nn)]-h
sub.tree<-pbtree(n=length(jj),scale=h,tip.label=species[jj])
if (method == "random"){
h <- runif(n = 1) * tree$edge.length[which(tree$edge[,2] == nn)]
tree$edge.length[which(tree$edge[, 2] == nn)] <- tree$edge.length[which(tree$edge[, 2] == nn)] - h
sub.tree <- pbtree(n = length(jj), scale = h, tip.label = species[jj])
} else {
sub.tree <- stree(length(jj), tip.label = species[jj])
}
tree<-bind.tree(tree,sub.tree,where=nn)
} else if(length(jj)==1) tree$tip.label[nn]<-species[jj]
}
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