[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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