Dear Patrick,
Yes, many, many examples could be cited, and I'll add a couple of my own below.
More generally, though, remember that there is generally nothing magic about
phylogenetically informed statistical methods, such as so-called PGLS.
PGLS is just GLS done with use of phylogenetic information.
And GLS is just OLS with some assumptions relaxed.
(Of course, optimal estimation may get a little more complicated in some cases.)
And don't forget that PGLS is the same as Felsenstein's (1985) phylogenetically
independent contrasts!
(Not including more complicated models that estimate optimal transformations of
phylogenetic branch lengths.)
Garland, Jr., T., and A. R. Ives. 2000. Using the past to predict the present:
confidence intervals for regression equations in phylogenetic comparative
methods. American Naturalist 155:346–364.
Gartner, G. E. A., J. W. Hicks, P. R. Manzani, D. V. Andrade, A. S. Abe, T.
Wang, S. M. Secor, and T. Garland Jr. 2010. Phylogeny, ecology, and heart
position in snakes. Physiological and Biochemical Zoology 83:43–54.
Blomberg, S. P., J. G. Lefevre, J. A. Wells, and M. Waterhouse. 2012.
Independent contrasts and PGLS regression estimators are equivalent. Systematic
Biology 61:382–391.
Cheers,
Ted
Theodore Garland, Jr., Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Facsimile: (951) 827-4286 (not confidential)
Email: tgarl...@ucr.edu
http://www.biology.ucr.edu/people/faculty/Garland.html
http://scholar.google.com/citations?hl=enuser=iSSbrhwJ
Director, UCR Institute for the Development of Educational Applications
Editor in Chief, Physiological and Biochemical Zoology
Fail Lab: Episode One
http://testtube.com/faillab/zoochosis-episode-one-evolution
http://www.youtube.com/watch?v=c0msBWyTzU0
From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Chris Organ
[organch...@gmail.com]
Sent: Saturday, August 08, 2015 8:48 AM
To: Patrick Gemmell; r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] PGLS multiple regression with dummy variables and
interaction terms
Dear Patrick,
Sure - see the following as an example (using BayesTraits, but easily
done in R too):
Organ, C. L., A. Canoville, R. R. Reisz, and M. Laurin. (2011).
Paleogenomic data suggest mammal-like genome size in the ancestral
amniote and derived large genome size in amphibians. Journal of
Evolutionary Biology. 24: 372–380.
Best, Chris
_
Chris Organ
Department of Microbiology and Immunology
Department of Earth Sciences
Montana State University, Bozeman, MT 59717
or...@montana.edu
www.organlab.net
On Fri, Aug 7, 2015 at 11:06 AM, Patrick Gemmell
patrick.gemm...@dtc.ox.ac.uk wrote:
Dear R-sig-phylo list,
I have a non-phylogenetic multiple regression y ~ x1 + ... + xn + d1 + d2 +
d3, where x1 ... xn are continuous variables and d1, d2 and d3 are dummy
variables (i.e. for each species in the tree I may have up to 4 data points).
In fact, sometimes my dummy variables interact with my continuous variables.
Can I perform a similar multiple regression using the PGLS method? I am very
new to phylogenetic analysis with R, but it seems that both caper and ape
need to assign tip labels to row names, and of course, such row names would
not be unique and therefore make R unhappy.
Any advice would be appreciated. Thank you for your time.
-- Patrick
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