Hi Gabriel.
You could try the following, which worked for me with a simulated tree
containing 9898 tips, 7898 of which were extinct:
library(phytools)
obj-drop.tip(tree,getExtinct(tree))
obj
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 9/30/2014 6:44 AM, Gabriel Yedid wrote:
Hello all,
I am trying to drop extinct taxa from a large phylogeny generated with
a non-R-based tree simulation program. The tree was saved in a Nexus
file which was read in with read.nexus. It's quite large--10911
leaves, but only 2055 are alive i.e. lineages that survived to the
end of the simulation. It's these lineages I want to keep around for
further analysis.
I've tried both the drop.fossil (from APE) and drop.extinct(from
geiger) functions, but both of them give problems. If I use the
customary low tolerance for either of these functions, drop.fossil
produces the following error:
INTREE_EXTANT = drop.fossil(INTREE, tol=1e-6)
Error in xmat[, 1] : incorrect number of dimensions
Lowering the tolerance value to 1e-4 trims off some of the living tips
I wanted kept (the resulting tree is smaller than it's supposed to
be).
drop.extinct just seems to hang and doesn't return even after about 10
minutes, no matter what tolerance value I supply.
Is there some other way I can remove extinct lineages from a large
tree like this?
cheers,
Gabe
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