-project.org
Subject: Re: [R-sig-phylo] variation in rates over time, unexpected
message when using Brownie.lite
That's a fairly small tree to be doing this with -- an old rule of thumb (I
think from Pagel) is 20 tips per parameter. Common issues are zero length
(or effectively zero length) branch
Dear List,
taking advantage of the discussion, I'd like to ask if I could do these
test of rate heterogeneity in brownie.lite or auteur with a polytomous
tree. Apparantly, auteur only accepts a fully dichotomous tree. Is there
any alternative?
Thank you in advance,
Diogo
--
Atenciosamente,
] variation in rates over time
Message-ID:
cakywhkq-jjroqzdvfutphi4xopxam+aaacu64nldb3inxoz...@mail.gmail.com
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I agree with the suggestions so far. I just wanted to point out a few more
alternatives:
You could use the geiger package to estimate the best scaling
, Jason S jas2...@yahoo.com wrote:
Thanks, guys. That's exactly what I needed.
From: Liam J. Revell liam.rev...@umb.edu
To: Matt Pennell mwpenn...@gmail.com
-project.org
Sent: Monday, September 17, 2012 9:22 PM
Subject: Re: [R-sig-phylo] variation in rates over
Jason,
I think the best way to do this is with the approach of O'Meara et al. 2006
Evolution Brownie.
Liam Revell has implemented this in R in his package phytools. You can
modify the steps taken in this tutorial here
http://phytools.blogspot.com/2011/07/running-brownielite-for-arbitrarily.html
Hi Jason. Matt is absolutely correct. You can do this with phytools.
Say, for instance, you have an ultrametric phylogeny with branches in
millions of years (tree) and data vector containing the trait values for
species (x) and you want to test the hypothesis that the last 3.4 my has
a
Thanks, guys. That's exactly what I needed.
From: Liam J. Revell liam.rev...@umb.edu
To: Matt Pennell mwpenn...@gmail.com
-project.org
Sent: Monday, September 17, 2012 9:22 PM
Subject: Re: [R-sig-phylo] variation in rates over time
Hi Jason. Matt
. Revell liam.rev...@umb.edu
To: Matt Pennell mwpenn...@gmail.com
-project.org
Sent: Monday, September 17, 2012 9:22 PM
Subject: Re: [R-sig-phylo] variation in rates over time
Hi Jason. Matt is absolutely correct. You can do this with phytools.
Say, for instance, you have an ultrametric phylogeny
