Hello, I agree with Joe that Pagel’s 1994 method might be a good option to analyze the data. I would only include a word of caution that the method can be sensitive to the sample sizes in each of the states (i.e. 0,0 ; 0,1 ; 1,1 ; 1,0 : environment yes/no & degrades carbon yes/no) so you should take this into account - if it applies - when interpreting your results.
Cheers Alejandro _______________________________________________ Dr Alejandro Gonzalez Voyer Laboratorio de Conducta Animal Instituto de Ecología Circuito Exterior S/N Ciudad Universitaria Universidad Nacional Autónoma de México México, D.F. 04510 México Tel: +52 55 5622 9044 E-mail: alejandro.gonza...@iecologia.unam.mx Web: www.alejandrogonzalezvoyer.com > El 10/02/2016, a las 11:41, Heath Blackmon <coleo...@gmail.com> escribió: > > 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/
