Hi,
Do you have a software program for plug and ply to measure phylogenetic signal
in a phylogenetic tree? I have a very high signal in an extinct species that
is represented in a morphology matrix but not in the molecular sequence matrix,
yet it appears to have the highest phylogenetic
From: Alberto Gallano alberto@gmail.com
Subject: Re: [R-sig-phylo] How to detect phylogenetic signal
(lambda) in one unscaled trait?
To: Alejandro Gonzalez alejandro.gonza...@ebd.csic.es
Cc: R-phylo Mailing-list r-sig-phylo@r-project.org
Thanks Alejandro,
yes, I see this difference. I
to then analyze
a trait that is no longer correlated with body size.
Cheers,
Ted
Original message
Date: Wed, 23 Mar 2011 02:13:36 +0200
From: Alberto Gallano alberto@gmail.com
Subject: Re: [R-sig-phylo] How to detect phylogenetic signal
(lambda) in one unscaled trait?
To: Alejandro
This is a repost of an earlier question, after my colleague helped me with
my English:
To calculate signal in PGLS multiple regression (with say two independent
variables) I can use the following model:
lambdaModel - gls(Y ~ X + bodymass, correlation=corPagel(1, tree),
method=ML)
This will
Subject: [R-sig-phylo] How to detect phylogenetic signal (lambda) in
one unscaled trait?
To: r-sig-phylo@r-project.org
This is a repost of an earlier question, after my colleague helped
me with
my English:
To calculate signal in PGLS multiple regression (with say two
statistic.
Cheers,
Ted
Original message
Date: Tue, 22 Mar 2011 20:37:58 +0200
From: Alberto Gallano alberto@gmail.com
Subject: [R-sig-phylo] How to detect phylogenetic signal (lambda) in
one unscaled trait?
To: r-sig-phylo@r-project.org
of that quantity.
4. Compute the K statistic.
Cheers,
Ted
Original message
Date: Tue, 22 Mar 2011 20:37:58 +0200
From: Alberto Gallano alberto@gmail.com
Subject: [R-sig-phylo] How to detect phylogenetic signal (lambda
Ted wrote:
Following on that, various papers (I can't remember the references)
have argued that imagining Brownian-like evolution of body size on a
log scale seems reasonable. That is, it should be equally easy for an
elephant's body size to evolve 10% as for a mouse's body size to
evolve
Hi Alberto,
The results differ between the two approaches because you're actually
estimating two different things.
gls(logY ~ logX, correlation=corPagel(1, tree), method=ML)
Will give you the estimate of lambda for the residuals of the fitted model.
while:
fitContinuous(tree, log(Y/X),
Thanks Alejandro,
yes, I see this difference. I think my question is: if the goal is to assess
phylogenetic signal in a trait, after accounting for interspecific
differences in body size, which of these two alternatives is preferable?
They both seem to calculate lambda after correcting for body
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