Hi All
I have a large dataset and a large tree, however the intersection between them
both is quite low. As a supplement to analyses solely on the species that
appear in both the dataset and the tree I thought I could take the species that
are present in the dataset and not the tree, and add
Something similar to this is in phytools
(http://blog.phytools.org/2013/11/new-function-to-add-species-to-genus-in.html),
though not yet on CRAN. Let me know if this is what you're thinking of.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
Hi,
There is also the stickTip function:
http://rleca.pbworks.com/w/file/fetch/40813743/stickTips_1.2.html
it is possible to tweak the code for more specific things...
Best,
Julien
From: liam.rev...@umb.edu
Date: Tue, 25 Feb 2014 10:32:36 -0500
To: h.ferguson-...@ucl.ac.uk;
At the risk of inundating you with options, Henry, there is also
expandTaxonTree in the package paleotree (on CRAN) which is similar to the
above, but also lets you collapse higher taxa you list as paraphyletic,
which can be useful if the taxonomic work of your group has never been
concerned with
Hi all,
I have an issue with using the drop.random to drop taxa from a set of
simulated trees. When I try to give the list as input it shows an
error:
Error in drop.random(simtrees, 937) :
object phy is not of class phylo
I also tried using lapply and it keeps showing the same message.
Hi Juanita
try:
lapply(simtrees, drop.random, n = 937)
when using lapply (or any of the apply family) you need to specify additional
arguments taken by the function youre applying by name, along with their
values.
graham
Graham
