Re: [R-sig-phylo] collapse.singles() can be confused by node numbering (Was: Bug in reorder.phylo() (related to cleaning phylo objects))

Hi David, You are right. There is even a simpler example of this problem with the following tree (tb): tb$edge [,1] [,2] [1,]46 [2,]61 [3,]65 [4,]53 [5,]52 tb$tip.label [1] A B C tb$Nnode [1] 3 Giving similar outputs to what you report below:

[R-sig-phylo] collapse.singles() can be confused by node numbering (Was: Bug in reorder.phylo() (related to cleaning phylo objects))

Hello all, Following up on discussion from Monday, I've been trying to figure out how the tree I shared broke ape's rules for 'phylo' objects. It turns out, it doesn't, really (other than having single nodes), at least not as defined by checkValidPhylo or as described in the formatTree PDF.