[R-sig-phylo] edge representation of trees produced by birthdeath.tree() in geiger

2011-09-09 Thread Andrew Barr
Hi all, While simulating some trees using the birthdeath.tree() function in geiger I noticed an inconsistency between the node/tip labels in the edge matrix and in a plot of the tree. I dumped in the text of one of the trees I produced as an example. library(ape)

Re: [R-sig-phylo] edge representation of trees produced by birthdeath.tree() in geiger

2011-09-09 Thread Liam J. Revell
Hi Andrew. This is because the numbers in tre$edge are node tip numbers, not tip labels (which also can be numbers). The translation between tip numbers and tip labels is given by tre$tip.label. Here, tip labels are indexed by their numbers in tre$edge. For instance, in your case we