I could not have said it better myself!
Thanks, Luke!
Ted
From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on
behalf of Luke Matthews [lmatth...@activatenetworks.net]
Sent: Thursday, January 19, 2012 6:41 AM
To: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] R-sig-phylo Digest, Vol 48, Issue 12
Ana,
I think what Ted and Paolo are getting at is you can't say the evolutionary
relationships contributed to X% of the slope because the tree only deals with
the nonindependence of the data points and is not itself an independent
predictor variable. Because of this, regular gls regression applied to data
that are nonindependent due to phylogeny produce unbiased estimates of the
slope. The estimates of the standard error of the slopes, however, are biased
to be too small when you run gls with nonindependent data.
You are correct, however, that using a phylogeny will almost always alter the
slope. This is because phylogenetic comparative methods (PCM) model the
structure of the nonindependence and so change the slope estimate. This makes
PCM and related methods (spatial models, network models) quite different from
some methods of rank or robust regression that can produce exactly the same
slope estimates as gls and will only increase the standard error estimates. In
your particular case, the slope was higher. So it would be accurate to say, in
this particular case, that ignoring the phylogeny resulted in a slope that was
underestimated (not biased) by 26%. The phylogeny does not 'account for' this
% of slope, but ignoring the phylogeny does produce a slope estimate that is
inaccurate by 26% of the better PIC slope in this particular case.
Best regards,
Luke
Luke J. Matthews
Director of Data Analysis
Activate Networks, Inc.
Message: 3
Date: Wed, 18 Jan 2012 17:34:14 +0100 (CET)
From: ppi...@uniroma3.it
To: "Theodore Garland Jr" <theodore.garl...@ucr.edu>
Cc: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org>, Ana Longo
<ana.lo...@gmail.com>
Subject: Re: [R-sig-phylo] Comparing slopes from regressions and PIC
regressions
Message-ID: <2397.79.32.224.88.1326904454.squir...@mail.uniroma3.it>
Content-Type: text/plain;charset=iso-8859-1
VERY synthetically....
The two r-squared are NOT comparable. Taking in to account phylogeny is useful
just to partial out data non independence due to shared ancestry, and to
perform better tests of significance but the r-sq could be higher or smaller
just because of chance.
Maybe someone can add more on this.
best
paolo
Long story short, you don't want to think about it in those terms.
Cheers,
Ted
Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Wet Lab Phone: (951) 827-5724
Dry Lab Phone: (951) 827-4026
Home Phone: (951) 328-0820
Facsimile: (951) 827-4286 = Dept. office (not
confidential)
Email: tgarl...@ucr.edu
http://www.biology.ucr.edu/people/faculty/Garland.html
Experimental Evolution: Concepts, Methods, and Applications of Selection
Experiments Edited by Theodore Garland, Jr. and Michael R. Rose
http://www.ucpress.edu/book.php?isbn=9780520261808
(PDFs of chapters are available from me or from the individual authors)
________________________________________
From: r-sig-phylo-boun...@r-project.org
[r-sig-phylo-boun...@r-project.org] on behalf of Ana Longo [ana.lo...@gmail.com]
Sent: Wednesday, January 18, 2012 7:20 AM
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] Comparing slopes from regressions and PIC regressions
Dear all
I am currently analyzing a community dataset of two continuous traits ?
survival and disease resistance.
I ran two regressions: (1) considering each species independent data points,
and (2) phylogenetic independent contrasts.
Both regressions were
significant. Blomberg?s K also significant and ~ 0.38, and 0.34, respectively.
However, I am interested in the slope of these regressions. For regression 1,
slope = 0.142, for regression 2 slope = 0.105.
I am interested in saying how much (in %) the evolutionary relationships
contributed to the slope. My question is:
Can I say that evolutionary relationships accounted for 74% (0.105/0.142) of
the observed slope? Or is it only 26%?
Thanks in advance for your help, since I don't have any experience running
these types of analyses.
Best regards,
Ana
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--
Paolo Piras
Center for Evolutionary Ecology
and
Dipartimento di Scienze Geologiche, Universit? Roma Tre Largo San Leonardo
Murialdo, 1, 00146 Roma
Tel: +390657338000
email: ppi...@uniroma3.it
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