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? -- View this message in context: http://r.789695.n4.nabble.com/Discrete-trait-Ornstein-Uhlenbeck-in-R-tp4649356.html Sent from the R help mailing list archive at Nabble.com.
Discrete trait Ornstein–Uhlenbeck in R?
4 messages · Jeff Newmiller, Ben Bolker, KRAmazon
I don't know anything about your subject, but have you reviewed
RSiteSearch("ornstein uhlenbeck")
?
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KRAmazon <sjdavid at alumni.uci.edu> wrote:
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? -- View this message in context: http://r.789695.n4.nabble.com/Discrete-trait-Ornstein-Uhlenbeck-in-R-tp4649356.html Sent from the R help mailing list archive at Nabble.com.
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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
7 days later
Thanks for the feedback. By discrete, I meant a categorical trait (diel activity). I've looked at the discrete models in geiger, but I had to ask about Ornstein-Uhlenbeck because one of my advisors suggested it. -- View this message in context: http://r.789695.n4.nabble.com/Discrete-trait-Ornstein-Uhlenbeck-in-R-tp4649356p4650249.html Sent from the R help mailing list archive at Nabble.com.