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$edge[,1]) is 33. When I try to execute your loop,
this happens:
> extract.clade(phy, 18)
Phylogenetic tree with 17 tips and 16
Hi all,
I would like to break a phylogenetic tree into all possible clades and then
examine each one of them for certain characteristics.
I am writing some code to do this from scratch, but it’s getting pretty
cumbersome quickly.
I was wondering whether there are some functions out there
Not sure if I understand the problem completely, but this should allow you to
examine all of the clades (and should work if polytomies are involved):
# for tree phy
rootID <- length(phy$tip.label) + 1;
for (i in rootID:max(phy$edge[,1])) {
clade <- extract.clade(phy, i);
# do something
}
Hmm. Maybe something wonky with your tree? I simulated a 17-tip tree and tried
things out:
phy <- rtree(17);
rootID <- length(phy$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
