William Gearty -- > > Thank you Don and Julien for your suggestions. I was able to run threshml > using Rthreshml from the Rphylip package. However, now I'm not really sure > what to do with the results. Can I use the output to perform ancestral > state reconstruction/estimation for the continuous (3) and discrete (1) > characters? I see that phytools has ancThresh, but that only seems to work > with a single character.
I don't know what are the limitations of Rphylip's interface with Threshml, but I can address Threshml itself -- as I wrote it. In principle the liabilities sampled at the interior nodes of the tree could be used to do ancestral reconstructions at those nodes, in a very straight- forward way. Just consider them, not the rest of the tree, and make a histogram of them at the node. However I never bothered to put in any interface to do that. However note that what Threshml does is to transform the liabilities to independent variables, using the current best estimate of the covariance matrix of liabilities. The Gibbs sampling (and at the tips, the Metropolis/Hastings sampling) occurs in the independent characters. Then you have to transform back to the liabilities before you have samples for those at the interior nodes. So matters are not simple, but in principle it can be done. Note that for continuous traits Threshml can also be used to sample values at the interior nodes. Of course this is a lot more computation than just using likelihood computations -- I've checked and the sampling does infer the same covariances in that case. In this all-continuous case the same issue of transforming to independent characters also comes up. 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 _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
