It's hard to tell what you did exactly. Did you do:
mytree <- compute.brlen(mytree)
? That should have worked. I've cc'ed this message to r-sig-phylo, which
is the more appropriate forum.
Cheers,
Simon.
On 10/03/15 07:05, Beth Williams wrote:
Dear All,
I am having some trouble with R and would be extremely grateful if anyone has a way around this. I have loaded a nexus
tree from PAUP into R using the command read.nexus and this loaded, it was reported as "rooted; with no branch
lengths". I then used the command "compute.brlen(mytree)" to compute the branch lengths and this was
reported as "rooted; includes branch lengths". I added my community data (samp) and then tried to compute the
phylogenetic diversity with the command "> pd(samp, mytree, include.root=TRUE)" however it said it could not
calculate the PD as there were no branch lengths. Is there a way to incorporate the branch lengths into the calculation
for PD?
Thanks for your time,
Beth
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Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat.
Senior Lecturer and Consultant Statistician
School of Biological Sciences
The University of Queensland
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