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 [[alternative HTML version deleted]] ______________________________________________ r-h...@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
-- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Senior Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au http://www.evolutionarystatistics.org Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. Basically, I'm not interested in doing research and I never have been. I'm interested in understanding, which is quite a different thing. - David Blackwell _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/