Hello Frank,
Frank Burbrink wrote on 06/07/2011 21:06:
Hello All,
I have some large code that simulates gene trees from species trees and I
need to automate the production of chronograms in R. I have used the
"chronopl" function in Ape and can automate that just fine. However, I am
at a loss as to how to get the cross validation procedure for estimating the
proper lambda to work in that function. Any help would be appreciated.
There is a bug in this function happening when an interval calibration
is used instead of a fixed date. The corrected version is on ape's SVN:
https://svn.mpl.ird.fr/ape/dev/ape/R/chronopl.R
(with the current version the CV analysis returns 0's)
Does this solve your problem?
Also, does there exist a Bayesian relaxed clock (or relaxed phylogenetics)
method available in R?
See the package LAGOPUS by Christoph Heibl on his web site.
Best,
Emmanuel
Thanks!
Frank
--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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