Also see BayesTraits for the bayesian version. Jake > On May 3, 2016, at 8:11 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > > Hi Michael. > > This is essentially the method of Pagel (1994). Though often interpreted as a > test for correlated evolution of two binary characters, the model that is > actually being fit is one in which the rate of transition 0->1 (or vice > versa) in character A is affected by the state of binary character B; or, > conversely, if the rate of transition 0->1 (or vice versa) in character B is > affected by the state of character A. > > This is implemented in fitPagel of phytools and I believe that this & other > more sophisticated flavor are available as part of the package corHMM. > > 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 5/3/2016 8:00 PM, Michael Foisy wrote: >> Hello, >> >> Quick question. I'm interested in whether the presence/absence of character >> 'A' affects the rate of evolution in character 'B'. Is there a function >> that will do this for two or more discrete characters? >> >> I've seen ratebystate {phytools} for continuous data; but my data are all >> binary! >> >> >> Thank you! >> , Michael Foisy >> >> MSc. Student >> University of Toronto >> michael.fo...@mail.utoronto.ca >> >> >> [[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/
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