Dear Simon,
Simon Maccracken Stump wrote on 09/04/2011 00:37:
Dear everyone,
Good morning. I have been trying to run a phylogenetic independent
contrast in R using Phylocom, using a tree from Phylomatic. I am
having some difficulty, and was wondering if anyone could help.
Here is what I
Hi Emmanuel:
On Apr 11, 2011, at 12:55 AM, Emmanuel Paradis wrote:
You should not used the transformation suggested on this wiki (it is
a bit outdated, NPRS has been removed from ape). In most situations,
you should just leave S=1.
The wiki can be updated (by anyone, in fact). How would
Hi Emmanuel,
Many thanks for your suggestions. I think a group of us at Berkeley would
be very interested in working out different ways to simulate these processes
and then share our results. We'll keep you posted. I think starting with
rcoal and compute.brlen would be a great jumping off
Hi Andy,
Brian Sidlauskas did this in an Evolution paper in 2008 (based on Yang and
Rannala 1997):
Sidlauskas, Brian L. 2008. Continuous and arrested morphological
diversification in sister clades of characiform fishes: a phylomorphospace
approach. Evolution 62(12): 3135-3156.
He had a
Hi Andy,
Andy Rominger wrote on 11/04/2011 23:04:
Hi Emmanuel,
Many thanks for your suggestions. I think a group of us at Berkeley
would be very interested in working out different ways to simulate these
processes and then share our results. We'll keep you posted. I think
starting with
