Hi Dan, You might be interested in looking at my package mvSLOUCH ( http://cran.r-project.org/web/packages/mvSLOUCH/ ) and the paper : Krzysztof Bartoszek, Jason Pienaar, Petter Mostad, Staffan Andersson and Thomas F. Hansen, A phylogenetic comparative method for studying multivariate adaptation Journal of Theoretical Biology, 314:204-215, 2012.
Your categorical predictors will be the regimes (but as you have two you will have to paint distinct pairs on the tree). I hope this will be helpful? Best wishes! Krzysztof Bartoszek _______________________________________________ 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/
