Hi Peter.
I'm not sure if this is what you mean, but Felsenstein (2005, 2012) has
a method for estimating the correlation between discrete characters or a
discrete and a continuous character in which the discrete trait is
modeled using the threshold model from quantitative genetics. There is a
stand-alone program for this called Threshml
(http://evolution.gs.washington.edu/phylip/download/threshml/). I have a
Bayesian MCMC version in the phytools package called threshBayes
(http://blog.phytools.org/search?q=threshBayes). So far, threshBayes
only allows binary discrete characters & two traits; Threshml can
analyze more than two traits - but I believe is still limited to binary
discrete characters. Please let me know if it would be helpful to your
research to extend threshBayes to allow for multistate (ordered,
naturally) discrete characters.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 4/7/2013 6:35 PM, New Bio wrote:
Dear all,
Just started studying phylogeny. I know BayesTraits program can calculate
the likelihood of the observed data given the model of two charaters evolve
dependently or independently. I am wondering how to do it with R packages
or functions for discrete and continuous characters?
Best,
Peter
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