A phytools user asks:
"I have a list of names that correspond exactly to the tips of a phylogenetic tree. What i'd like to do is obtain the branch lengths that correspond to these tip edges."
This can be done with one line:
n<-length(tree$tip.label)
ee<-setNames(tree$edge.length[sapply(1:n,function(x,y) which(y==x),y=tree$edge[,2])],tree$tip.label)
(Or at least this would be one line if the width of this entry window permitted me to put length(tree$tip.label) into my sapply block instead of first calculating n.)ee<-setNames(tree$edge.length[sapply(1:n,function(x,y) which(y==x),y=tree$edge[,2])],tree$tip.label)
We get a vector with all the terminal edge lengths with names set to all the tip names in the tree, so we can rearrange or select a subset of these tip lengths on that basis.
Let's check it:
> tree<-pbtree(n=10)
> tree$edge.length<-round(tree$edge.length,3)
> n<-length(tree$tip.label)
> ee<-setNames(tree$edge.length[sapply(1:n,function(x,y) which(y==x),y=tree$edge[,2])],tree$tip.label)
> ee
t9 t10 t3 t4 t7 t8 t2 t1 t5 t6
0.262 0.262 0.587 0.587 0.385 0.385 0.641 0.727 0.432 0.432
> plotTree(tree)
> edgelabels(tree$edge.length)
> tree$edge.length<-round(tree$edge.length,3)
> n<-length(tree$tip.label)
> ee<-setNames(tree$edge.length[sapply(1:n,function(x,y) which(y==x),y=tree$edge[,2])],tree$tip.label)
> ee
t9 t10 t3 t4 t7 t8 t2 t1 t5 t6
0.262 0.262 0.587 0.587 0.385 0.385 0.641 0.727 0.432 0.432
> plotTree(tree)
> edgelabels(tree$edge.length)
