This is implemented in my "phytools" package. This is not yet on CRAN,
but can be downloaded from
http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/. The function is
ltt(). It is slow, but seems to work. Please let me know if you have
success with this.
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 8/10/2011 8:51 PM, Rob Lanfear wrote:
Hi All,
I have a set of simulated birth-death trees, which include extinct and
extant lineages. I'd like to see if my simulations are doing what I think
they should be, by plotting out the number of lineages through time.
Does anyone know of a method of doing this that incorporates extinct
lineages, i.e. one where the number of lineages can decrease as well as
increase through time.
I can see how it could be done (I think...) by making an ordered data frame
of node times (+1 lineage) and extinction events (-1 lineage), but it seems
like somebody might already have done it.
Cheers,
Rob
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