KRAmazon <sjdavid <at> alumni.uci.edu> writes: > Is there a package that will allow me to fit Brownian motion and > Ornstein–Uhlenbeck models of evolution for discrete traits? I know that > geiger and ouch have commands for fitting these models for continuous > traits, but these aren't suitable for discrete trait evolution, correct?
I'm not quite sure what the model would be, since Brownian and O-U models are (as far as I know) explicitly defined as models of continuous traits. The analogue of Brownian motion would presumably be a continuous-time neutral Markov chain on a discrete space ... (by "discrete" do you mean a trait such as microsatellite length, or a categorical trait, or ... ?) Have you checked the Phylogenetics task view <cran.r-project.org/web/views/Phylogenetics.html> ? It says that geiger fits discrete-trait models. If you don't get an answer here you might have better luck on the r-sig-ph...@r-project.org mailing list ... Ben Bolker ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
