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=en&user=iSSbrhwAAAAJ 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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
