oun...@r-project.org]
> on behalf of Brian O'Meara [bome...@utk.edu]
> Sent: Tuesday, September 18, 2012 1:25 PM
> To: Agus Camacho
> Cc: r-sig-phylo@r-project.org
> Subject: Re: [R-sig-phylo] variation in rates over time, unexpected
> message when using Brownie.lite
&g
While auteur will complain if given a polytomous tree, one can randomly
resolve the polytomies (using the multi2di function in ape, for
instance). The BM likelihoods of the data given any of the randomly
resolved trees will be identical. Be warned that if the polytomies are
soft, this will si
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,
*Diog
edu]
Sent: Tuesday, September 18, 2012 1:25 PM
To: Agus Camacho
Cc: r-sig-phylo@r-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)
ng with this topic.
>
> Cheers,
> Agus
>
> Message: 9
> Date: Tue, 18 Sep 2012 00:13:00 -0400
> From: "Brian O'Meara"
> To: Jason S
> Cc: "R-sig-phylo@r-project.org"
> Subject: Re: [R-sig-phylo] variation in rates over time
> Message-ID:
gest of
the mail list, without leaving the thread?
Below, I pasted the complete thread dealing with this topic.
Cheers,
Agus
Message: 9
Date: Tue, 18 Sep 2012 00:13:00 -0400
From: "Brian O'Meara"
To: Jason S
Cc: "R-sig-phylo@r-project.org"
Subject: Re
f
the mail list, without leaving the thread?
Below, I pasted the complete thread dealing with this topic.
Cheers,
Agus
Message: 9
Date: Tue, 18 Sep 2012 00:13:00 -0400
From: "Brian O'Meara"
To: Jason S
Cc: "R-sig-phylo@r-project.org"
Subject: Re: [R-sig-phylo]
> From: Liam J. Revell
> To: Matt Pennell
>
> -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, fo
Thanks, guys. That's exactly what I needed.
From: Liam J. Revell
To: Matt Pennell
-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 t
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 differen
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
Hello,
I see that there are several interesting alternatives to test for different
rates among clades. However, I was wondering if there is a method to test for
varying rates over time. I'm aware of Pagel's delta and the EB model, but I was
thinking more in terms of testing if there is a diff
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