Hi John, In addition to Brian's suggestion, depending on what you are interested in testing you could also set this up in GLM-style format either with the binary trait as the response in a package like phylolm or as a phylogenetic mixed model in ape (with the binary trait as response) or MCMCglmm (with either trait as response).
Cheers, Kev Dr Kevin Arbuckle Darlithydd mewn Biowyddorau (Bioleg Esblygiadol) / Lecturer in Biosciences (Evolutionary Biology) Adran Biowyddorau / Department of Biosciences Coleg Gwyddoniaeth / College of Science Prifysgol Abertawe / Swansea University Abertawe / Swansea SA2 8PP UK Rhowch wybod i ni os hoffech dderbyn eich gohebiaeth yn Gymraeg. Rydym yn croesawu gohebiaeth yn Gymraeg neu yn Saesneg. Ni fydd gohebu yn Gymraeg yn arwain at oedi. -----Original Message----- From: R-sig-phylo [mailto:r-sig-phylo-boun...@r-project.org] On Behalf Of r-sig-phylo-requ...@r-project.org Sent: 22 March 2018 11:00 To: r-sig-phylo@r-project.org Subject: R-sig-phylo Digest, Vol 122, Issue 7 Send R-sig-phylo mailing list submissions to r-sig-phylo@r-project.org To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/r-sig-phylo or, via email, send a message with subject or body 'help' to r-sig-phylo-requ...@r-project.org You can reach the person managing the list at r-sig-phylo-ow...@r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of R-sig-phylo digest..." Today's Topics: 1. correlation of binary and multistate (John Denton) 2. Re: correlation of binary and multistate (Brian O'Meara) ---------------------------------------------------------------------- Message: 1 Date: Wed, 21 Mar 2018 19:19:55 +0000 From: John Denton <jden...@amnh.org> To: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org> Subject: [R-sig-phylo] correlation of binary and multistate Message-ID: <71f19d34-03a0-4121-a389-f7fe607b9...@amnh.org> Content-Type: text/plain; charset="us-ascii" 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 ------------------------------ Message: 2 Date: Wed, 21 Mar 2018 15:43:35 -0400 From: "Brian O'Meara" <omeara.br...@gmail.com> To: John Denton <jden...@amnh.org> Cc: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org> Subject: Re: [R-sig-phylo] correlation of binary and multistate Message-ID: <cakywhkoayv28kqbfi_pxmtjehdpopfkfly2dakocfzucs4y...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" 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 00->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]] ------------------------------ Subject: Digest Footer _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ------------------------------ End of R-sig-phylo Digest, Vol 122, Issue 7 _______________________________________________ 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/
