Simon Blomberg s.blomberg1 at uq.edu.au
Tue Mar 10 01:21:33 CET 2015

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.



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-help at 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
T: +61 7 3365 2506
email: S.Blomberg1_at_uq.edu.au

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

More information about the R-help mailing list