Following on from what Ted just said about size-correction - one can use a phylogenetic regression (GLS) with the trait of interest as the dependent variable and size as the independent variable, while simultaneously estimating lambda. The program BayesTraits can do this ( http://www.evolution.rdg.ac.uk/BayesTraitsV3.0.1/BayesTraitsV3.0.1.html) and I think the pgls function in the caper R package should be also able to do this if I recall correctly.
thanks, Manabu On Fri, 13 Jul 2018 at 20:43, Theodore Garland <theodore.garl...@ucr.edu> wrote: > I agree with everything that Liam wrote -- right on. > > Another point is that if you are looking at morphometric traits, then most > of them are probably highly positively correlated with body size. In that > case, testing for phylogenetic signal in, say, wing length, is going to be > largely redundant with testing for signal in body mass. Hence, for your > traits other than body size, you may want to analyze size-corrected values, > as described here: > > Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for > phylogenetic signal in comparative data: behavioral traits are more labile. > Evolution 57:717–745. > > Cheers, > Ted > > > Theodore Garland, Jr., Distinguished Professor > > Department of Evolution, Ecology, and Organismal Biology (EEOB) > > 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 > <http://idea.ucr.edu/>Educational > Applications <http://idea.ucr.edu/> > > > Editor in Chief, *Physiological and Biochemical Zoology > <http://www.press.uchicago.edu/ucp/journals/journal/pbz.html>* > > > Fail Lab: Episode One > > *https://www.youtube.com/watch?v=c0msBWyTzU0 > <https://www.youtube.com/watch?v=c0msBWyTzU0>* > > On Fri, Jul 13, 2018 at 12:29 PM, Liam J. Revell <liam.rev...@umb.edu> > wrote: > > > Dear Alyson. > > > > There is no general rule about this; however, my suggestion would be to > > use log-scaled values. This is because on a log-scale proportional > changes > > in the trait are equal, independent of the magnitude of the trait. That > is, > > a change of 1% in mass of whale is the same as a change in 1% in mass of > a > > mouse. If your analysis includes both mice and whales, then on the > original > > scale mice may appear to be changing very little in mass, while whales > > change a great deal - even if (relative to their sizes) both groups are > > changing just as much. On the other hand, if your analysis is of only > > whales or only mice it will make relatively little difference whether you > > use log-scaled data or the original values. > > > > I hope this is of some help. All the best, Liam > > > > Liam J. Revell, Associate Professor of Biology > > University of Massachusetts Boston > > web: http://faculty.umb.edu/liam.revell/ > > > > On 7/13/2018 2:07 PM, Alyson Brokaw wrote: > > > >> Hello Everyone, > >> > >> I am working with a comparative dataset using bat morphometrics. As part > >> of > >> my analysis, I want to estimate the phylogenetic signal of my > variables. I > >> understand how to do this using R. My question is more specifically > about > >> what kind of data I should be using when calculating the estimates. > >> > >> For the purposes of my other analyses (linear regressions), I have > >> log-transformed my data to meet assumptions for normality. When > estimating > >> phylogenetic signal, should I use my non-transformed, raw variables or > the > >> transformed variables? I get slightly different outputs if I run both on > >> the same measure. My intuition is that using the raw values is more > >> interpretable, but figured I would ask some people with more experience. > >> > >> Thank you for your time. > >> > >> -Alyson > >> ____________________________________________________________ > >> > >> Alyson Brokaw > >> M.S. Candidate: Biology, Humboldt State University > >> Cornell University '11, Ecology and Evolutionary Biology > >> > >> LinkedIn Profile <http://www.linkedin.com/pub/alyson-brokaw/3a/704/820> > >> Follow my research journey here! <http://afbrokaw.wordpress.com/> > >> > >> [[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-ph...@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-ph...@r-project.org/ > > > > [[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/ > -- Manabu Sakamoto, PhD manabu.sakam...@gmail.com [[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/
