Re: [R-sig-phylo] Extract all possible clades from a tree

This new code works perfectly for me. Thanks so much everyone for helping me to solve this issue in record time! Kamila > On Jan 6, 2017, at 6:39 AM, Emmanuel Paradis wrote: > > I paste below the new code of extract.clade for those who want to try it. > > Best, > >

Re: [R-sig-phylo] Extract all possible clades from a tree

I paste below the new code of extract.clade for those who want to try it. Best, Emmanuel extract.clade <- function(phy, node, root.edge = 0, interactive = FALSE) { n <- length(phy$tip.label) if (interactive) {

Re: [R-sig-phylo] Extract all possible clades from a tree

Hi, Klaus is right: extract.clade() fails if the tree has been rooted with resolve.root = TRUE before. I'm going to rewrite the function calling drop.tip (which will be safer). In the meantime, Klaus's function should work for Kamila. Best, Emmanuel Le 06/01/2017 à 05:17, Klaus Schliep a

Re: [R-sig-phylo] Extract all possible clades from a tree

Hmm. Maybe something wonky with your tree? I simulated a 17-tip tree and tried things out: phy <- rtree(17); rootID <- length(phy$tip.label) + 1; counter <- 1; for (i in rootID:max(phy$edge[,1])) { clade <- extract.clade(phy, i); # do something. just printing clade properties here

Re: [R-sig-phylo] Extract all possible clades from a tree

Dear Joseph, thanks so much. This is exactly what I need! I am running into some problems that I don’t understand though. In my case, rootID is 18, and max(phy$edge[,1]) is 33. When I try to execute your loop, this happens: > extract.clade(phy, 18) Phylogenetic tree with 17 tips and 16

Re: [R-sig-phylo] Extract all possible clades from a tree

Not sure if I understand the problem completely, but this should allow you to examine all of the clades (and should work if polytomies are involved): # for tree phy rootID <- length(phy$tip.label) + 1; for (i in rootID:max(phy$edge[,1])) { clade <- extract.clade(phy, i); # do something }