[R-sig-phylo] How to detect phylogenetic signal (lambda) in one unscaled trait?
tgarland at ucr.edu
tgarland at ucr.edu
Wed Mar 23 00:07:21 CET 2011
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 10%, and to analyze that you want everybody on a log scale.
Extending this, you would want to use log(Y/X) or log(Y/[X raised to
some allometric slope]).
Cheers,
Ted
---- Original message ----
Date: Tue, 22 Mar 2011 15:56:24 -0700
From: Joe Felsenstein <joe at gs.washington.edu>
Subject: Re: [R-sig-phylo] How to detect phylogenetic signal
(lambda) in one unscaled trait?
To: Alberto Gallano <alberto.gc8 at gmail.com>
Cc: tgarland at ucr.edu, r-sig-phylo at r-project.org
>
>Alberto Gallano wrote:
>
>> I think I was not clear with what I said about the log
transformation, and I
>> see now what you mean about using log-log when using regression.
Though It
>> does seem to me that logging two variables in a ratio context:
>>
>> log(Y) / log(X)
>>
>> or
>>
>> log(Y / X)
>>
>> would influence phylogenetic signal levels greatly, since, while
the order
>> of trait means is maintained, the magnitude of differences
between trait
>> means is altered (means with higher values are dragged toward the
centre of
>> the distribution). I assume, then, that this is nothing to worry
about.
>
>The above two are *not* equivalent. If a trait is doing a Brownian
>Motion on the log scale, the latter, log(Y/X) is OK, as it is
equivalent
>to to log(Y) - log(X), a straightforward linear combination.
>
>But log(Y)/log(X) could get you into real trouble, particularly
>if X got near 1, in which case the ratio could blow up.
>
>Joe
>----
>Joe Felsenstein joe at gs.washington.edu
> Department of Genome Sciences and Department of Biology,
> University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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