There's also corDISC in corHMM (disclosure: I'm a coauthor on the package). It does Pagel 1994 with two or three binary characters, allows for user set root states (I believe the canonical Pagel (1994) assumes equal freq at the root, I don't know if phytools uses this same assumption [a lot of programs assume equilibrium freq]), and allows additional control over the rate matrix. However, it requires you to specify what sort of rate matrix you want (has equal rates, all rate different, etc., but you would have to specify the dependent model matrix): the phytools code seems to loop over the named Pagel matrices, which are a subset of the possible matrices. So, I'd summarize it as phytools being more turnkey, corHMM having more control but less easy to use.
Oh, and in either case, read this and be afraid before starting analyses: Maddison & FitzJohn, 2014: http://sysbio.oxfordjournals.org/content/64/1/127 . Best, Brian _______________________________________ Brian O'Meara Associate Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http://nimbios.org/postdocs/ Calendar: http://www.brianomeara.info/calendars/omeara On Wed, Feb 10, 2016 at 12:41 PM, Heath Blackmon <coleo...@gmail.com> wrote: > Grace, > > The package phytools includes a function fitPagel if that is the method > that you want to use. He has a post on his blog that discusses his > implementation so it won't be a black box for you: > > > http://blog.phytools.org/2014/12/r-function-for-pagels-1994-correlation.html > > cheers > > Heath > > On Wed, Feb 10, 2016 at 11:14 AM, Joe Felsenstein <j...@gs.washington.edu> > wrote: > > > I do not know offhand whether there is an R implementation, but how about > > Mark Pagel's 1994 method for testing whether two 0/1 characters changing > > along a ohylogeny are changing independently? > > > > J.F. > > ----- > > j...@gs.washington.edu > > Joe Felsenstein, Department of Genome Sciences and Department of Biology > > Box 355065, University of Washington, Seattle, WA 98195-5065 > > > > [[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/ > > > > > > -- > *Heath Blackmon, Ph.D.* > > *Postdoctoral Researcher* > *University of Minnesota* > *coleoguy.github.io <http://coleoguy.github.io>* > *@coleoguy* <https://twitter.com/coleoguy> > *Phone 682-444-0538* > > [[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/ > [[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/
