You will want to try Bayesian mixed modeling which can handle your species # problem by using “species” as a group level (i.e. “random”) effect. I would recommend r packages brms and MCMCglmm and their vignettes. Both have detailed “phylo” examples.
Maybe check out the r-sig-mixed-model listserv as well. Lots of similar questions and good advice show up on there. Good luck! Jon -- Jonathan A. Nations PhD Candidate Esselstyn Lab <http://www.museum.lsu.edu/esselstyn> Museum of Natural Sciences <http://sites01.lsu.edu/wp/mns> Louisiana State University [[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/
