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.
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