[R] Discrete trait Ornstein–Uhlenbeck in R?

[Ben Bolker]

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-phylo at r-project.org mailing list ...

  Ben Bolker