Hi Karla, The original simple way to compare two clades, using phylogenetically independent contrasts, is here. Newer methods may have higher power, but this method is straightforward.
Garland, Jr., T. 1992. Rate tests for phenotypic evolution using phylogenetically independent contrasts. The American Naturalist 140:509–519. Cheers, Ted Theodore Garland, Jr., Distinguished 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 <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 Sat, Jul 22, 2017 at 7:07 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > Hi Karla. > > This is not yet possible, but it would be straightforward to add. For > instance, we could let the user specify different models such as A==B!=C > vs. A!=B==C and so on, and then compare this models in a standard way. I > will try to do this soon and then get back to you & the list. > > All the best, > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 7/22/2017 8:51 PM, Karla Shikev wrote: > >> Thanks, Liam! >> >> Just a quick follow-up question: in the example I saw on your webpage >> (with >> three clades, one of which with a higher rate), how would you go about a >> sort of "post-hoc" test to determine which clades differ significantly >> from >> one another in their rates? >> >> Karla >> >> On Sat, Jul 22, 2017 at 4:13 PM, Liam J. Revell <liam.rev...@umb.edu> >> wrote: >> >> Hi Karla. >>> >>> phytools has a function called ratebytree for this. This essentially >>> corresponds to the 'censored' model of O'Meara et al. 2006, but we also >>> have a submitted manuscript describing it. I can send you that in a >>> second >>> email. >>> >>> For more information about using the function you can search for >>> 'ratebytree' on my blog, blog.phytools.org. >>> >>> All the best, Liam >>> >>> Liam J. Revell, Associate Professor of Biology >>> University of Massachusetts Boston >>> web: http://faculty.umb.edu/liam.revell/ >>> email: liam.rev...@umb.edu >>> blog: http://blog.phytools.org >>> >>> >>> On 7/22/2017 3:10 PM, Karla Shikev wrote: >>> >>> Dear all, >>>> >>>> I'd like to test whether the rate of evolution of a phenotypic trait >>>> (e.g. >>>> body size) is significantly different among distantly-related clades >>>> (e.g. >>>> mammals vs birds). I got tip data and completely resolved and >>>> callibrated >>>> trees. One possibility would be to estimate rates and their confidence >>>> intervals for each clade and to compare them directly, but I'm sure >>>> there's >>>> a more elegant way to do this. >>>> >>>> Karla >>>> >>>> [[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/ >>>> >>>> >>>> >> [[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/
