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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