Hi John.
The posterior sample of the relative positions of the thresholds (if
there is more than one) are output in the matrix "par", i.e.:
mcmc<-ancThresh(...)
mcmc$par ## contains the posterior sample of the thresholds
To get a visualization of the posterior density you can, for instance,
use stats function density with the column of interest from par as input.
Is that helpful? I hope a little bit.
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 5/2/2014 9:26 AM, John Denton wrote:
Hi folks,
I'm trying to generate the thresholds and liabilities plot, including the
posterior support values, from Revell (2014) Evolution 68(3), Figure 6B. Does
anybody have a script for this? I see the liabilities output from ancThresh(),
but no thresholds.
Thanks!
~John
John S. S. Denton, Ph.D.
Department of Vertebrate Paleontology
American Museum of Natural History
www.johnssdenton.com
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