Dear Sergio, I do not use R very much, relying instead on our Matlab programs that accompany Lavin et al. (2008):
Lavin S.R., W.H. Karasov, A.R. Ives, K.M. Middleton, and T. Garland Jr. 2008. Morphometrics of the avian small intestine compared with that of nonflying mammals: a phylogenetic approach. Physiological and Biochemical Zoology 81:526–550. I would strongly suggest that you read the appendix to this paper regarding methods, their history, and terminology. Note that a GLS model does not inherently use any kind of branch length transformation. It uses the tree as inputted. It is mathematically equivalent to Felsenstein's (1985) phylogenetically independent contrasts. It implicitly assumes character evolution (or residual character evolution) akin to Brownian motion. Once you start estimating some branch lengths transformation along with regression parameters, you have a different beast. See the appendix noted above and, for the original source of this sort of model, Grafen (1989). 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 Sergio Ferreira Cardoso [sff.card...@campus.fct.unl.pt] Sent: Sunday, April 12, 2015 12:47 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] PGLS transformations Hi everyone, I'm relatively new in phylogenetic comparative methods. I'm a little confused about branch length transformations. I'm using a tree with divergence time (My) as branch lengths. When I use corPagel, corGrafen or corMartins in R, the branch lengths, are the branch lengths automatically transformed? e.g., gr.mammals<-corGrafen(1,phylo,fixed=F); fit<-gls(FCL~logBodymass,correlation=gr.mammals,data=df,method="ML"). My question may sound a bit nonsense but I've seen in some papers (e.g., Spoor, F., Garland, T., Krovitz, G., Ryan, T. M., Silcox, M. T., & Walker, A. (2007). The primate semicircular canal system and locomotion. *Proceedings of the National Academy of Sciences*, *104*(26), 10808-10812.) the indication that a PGLS was made without branch transformation, but no reference is made to the model (maybe it's corBrownian). Thank you very much. Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. -------------------- Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal [[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/
