Hi William, If you want to perform a joint reconstruction of the ancestral states for both continuous and discrete traits (e.g. to look at the evolutionary correlations) I think that you should have a look at the threshold model of Felsenstein (a bivariate version is available in phytools; I also remember an Evolution meeting where E. Goolsby was working on an efficient implementation of the model). The model assumes that discrete traits are governed by a latent process which is continuous which makes possible to fit a multivariate model with other continuous traits (although maybe with a reduced power).
All the best, Julien _______________________________________________ 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/
