Liam & Maria,
Liam J. Revell wrote on 09/02/2010 04:24:
Try this:
# given an object of class "phylo" called tree
# 1. create vector for terminal edge lengths
terminal.edges<-matrix(NA,length(tree$tip.label));
# 2. copy terminal branches into vector
terminal.edges<-tree$edge.length[tree$edge[1:(2*length(tree$tip.label)-2),2]<=length(tree$tip.label)];
The above will work if 'tree' is rooted and fully dichotomous. I'd
rather do this:
# identifies your terminal branches with TRUE:
terms <- tree$edge[, 2] <= Ntip(tree)
terminal.edges <- tree$edge.length[terms]
Step 2 will erase a possibly existing 'terminal.edges' object, so step 1
is not needed.
# 3. label terminal branches by tip label
names(terminal.edges)<-tree$tip.label;
This might not work in all cases because the tips are not always ordered
1, 2, 3, ... along the second column of the edge matrix. So you may
reorder your labels first:
names(terminal.edges) <- tree$tip.label[tree$edge[terms, 2]]
HTH
Emmanuel
I think that should work.
- Liam
Liam J. Revell
NESCent, Duke University
web: http://anolis.oeb.harvard.edu/~liam/
NEW email: lrev...@nescent.org
mgavil2 wrote:
Dear All
I am trying to find a way to get a vector of only the terminal branch
length
for species in a phylogeny, but cant seem to find a way
any suggestions?
Best,
Maria Mercedes
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--
Emmanuel Paradis
IRD, Montpellier, France
ph: +33 (0)4 67 16 64 47
fax: +33 (0)4 67 16 64 40
http://ape.mpl.ird.fr/
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