[R] APE

Simon Blomberg
2015-03-10T00:21:33Z

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-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
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