I have code for this in my TreEvo package (on R-forge -- see
brownieneglnL in <http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/R/brownie.R?rev=2&root=treevo&view=markup
>) though note that the package itself is not all cleaned up into
install.packages()-ready form. You could also dig into geiger's
fitContinuous function and use that code (look for "foo" in
fitContinuous.R) -- OUCH must have similar code. Odd if there's
nothing more direct.
Best,
Brian
On Mar 19, 2010, at 9:47 PM, Carl Boettiger wrote:
Dear r-sig-phylo,
I'd like to be able to estimate the likelihood of a model with a given
Brownian rate parameter under a given data set. For OU models, this
can be
accomplished through the ouch package with the flag fit=FALSE.
However
there does not seem to be a corresponding option for Brownian motion
in
ouch/geiger/ape algorithms for fitting a Brownian motion model?
Perhaps
I've overlooked something?
-Carl
--
Carl Boettiger
Population Biology, UC Davis
http://two.ucdavis.edu/~cboettig
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Brian C. O'Meara
Asst. Prof., Dept. of Ecology and Evolutionary Biology
University of Tennessee, Knoxville
http://www.brianomeara.info
865-408-TREE (8733)
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