You can do this with corHMM by making an appropriate model with rayDISC. For example, if character A has states 0,1 and character B has states 0,1,2, you then recode this into a single multistate character:
00 -> 0 01 -> 1 02 -> 2 10 -> 3 11 -> 4 12 -> 5 and then create a rate matrix that matches your hypotheses (i.e., force the 00->10 rate [the 0->3 rate in the new coding] to be the same as the 01->11 and 02->12 rates (so that the state of the second character doesn't affect the rate of the first character) or and compare (or model average) with a model where they are free to vary). It wouldn't be hard to make a looping thing to do this automatically (Jeremy Beaulieu has for two and three binary trait correlation in the same package with corDISC but not for multistate yet) but as far as I know no one has (pull requests welcome!). There may also be this functionality in phytools: I remember some Pagel correlation work was added, but I don't know about its limitations with multistate. Best, Brian PS: Of course, with all this stuff, I now worry about the Maddison and FitzJohn issue: https://academic.oup.com/sysbio/article/64/1/127/2847997. _______________________________________________________________________ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>, and Feedback <http://brianomeara.info/teaching/feedback/> Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Director for Postdoctoral Activities, National Institute for Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS) On Wed, Mar 21, 2018 at 3:19 PM, John Denton <jden...@amnh.org> wrote: > Hi all, > > Does anybody know of a package that does character correlations between > binary and multistate characters (and even better with the possibility of > missing data)? > > Thanks! > > ~John > _______________________________________________ > 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/
