For correlations per se, please check this paper: Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Systematic Biology 56:252-270.
>And here comes my question: is it >allowed to calculate only PICs based on my tree for those traits having >a signal, and to calculate "pseudo-PICs" based on a star phylogeny >(independence between species) for those traits having no signal? This >would allow me to correct the "signal-traits" but leave the other ones >more or less as they are. The benefit: I then can correlate all traits >with each other. Obviously, it is possible to do this. A problem is that then the statistical model is unclear/confusing. >I could not find any reference doing this, and I wonder >whether this is legal? We have discussed this here: Garland, T., Jr., A. F. Bennett, and E. L. Rezende. 2005. Phylogenetic approaches in comparative physiology. Journal of Experimental Biology 208:3015-3035. Page 3032: "With IC, it is easier to employ different sets of branch lengths for different traits (e.g. Garland et al., 1992; Lovegrove, 2003; Rezende et al., 2004), which may be particularly useful when one trait does not actually show phylogenetic signal (e.g. Tieleman et al., 2003; Rheindt et al., 2004) and/or for traits that are only nuisance variables, such as details of measurement or calculation methods that differ among studies (e.g. Wolf et al., 1998; Perry and Garland, 2002; Rezende et al., 2004)." Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Skype: theodoregarland Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ Inquiry-based Middle School Lesson Plan: "Born to Run: Artificial Selection Lab" http://www.indiana.edu/~ensiweb/lessons/BornToRun.html ________________________________________ From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Anne Kempel [kem...@ips.unibe.ch] Sent: Wednesday, April 17, 2013 5:37 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] trait correlations with PICs Dear all, I am dealing with plant traits of different plant species (28 plant species), and aim to correlate all traits with each other. I have a tree of my species, and some of those traits do have a phylogenetic signal, but most don't. Since I do not know, which trait depends on whom, I favour to do correlations instead of regressions - that's why I would like to use Phylogenetic independent contrasts (PIC) instead of PGLS. I have the impression that it does not make sense to calculate PICs for traits that do not have a signal. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate "pseudo-PICs" based on a star phylogeny (independence between species) for those traits having no signal? This would allow me to correct the "signal-traits" but leave the other ones more or less as they are. The benefit: I then can correlate all traits with each other. I could not find any reference doing this, and I wonder whether this is legal? I am grateful for any comment and suggestion! Thanks a lot in advance and best wishes from Switzerland, Anne -- Dr. Anne Kempel Institute of Plant Sciences Altenbergrain 21 3013 Bern Switzerland _______________________________________________ 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/
