Just to clarify Joe's email - Threshml can be called using my package
with Scott Chamberlain called Rphylip (not phytools). It is on CRAN;
however, Rphylip is just a 'wrapper' for PHYLIP, which still needs to be
installed locally. In the future we may change Rphylip so that it is
packaged with the source code of PHYLIP and so it calls the C source
code directly, since I believe that PHYLIP's current license permits this.
A simpler, Bayesian MCMC implementation of the threshold model that
permits only two characters is also available in the function
threshBayes in the phytools package.
All the best, Liam
Liam J. Revell, Associate 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 4/8/2016 5:50 PM, Joe Felsenstein wrote:
Sean --
... or, if you want to do it *really correctly*, you can use the threshold
model of Sewall Wright for the discrete character and use the MCMC approach
that I proposed in 2012:
Felsenstein, J. 2012. A comparative method for both discrete and
continuous characters using the threshold model. American Naturalist 179:
145-156.
which is implemented in my program Threshml which can be called from Liam
Revell's Phytools R package. It also works for multiple threshold
characters and multiple continuous characters.
Joe
----
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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