[R-sig-phylo] Bayesian dating in R vs. Multidivtime

2010-01-26 Thread Emmanuel Paradis
Dear all, I'm planning to do some molecular dating using Bayesian methods, ie, what people usually do with Multidivtime. After reading the doc of Multidivtime, I'm thinking to do my own implementation in R since it is straightforward to specify priors, define and run the Markov chain, and

Re: [R-sig-phylo] Bayesian dating in R vs. Multidivtime

2010-01-26 Thread Brian O'Meara
Emmanuel, you should check Lagopus (http://www.christophheibl.de/mdt/mdtinr.html ), which seems to connect R with multidivtime (based on documentation -- I haven't used it). Best, Brian On Jan 26, 2010, at 11:19 AM, Emmanuel Paradis wrote: Dear all, I'm planning to do some molecular

[R-sig-phylo] Transforming a data.frame into a phylogenetic tree

2010-01-26 Thread Timothee POISOT
Dear users, I am currently doing a model of community assembly, and I would like to integrate phylogenetic information. For each organism, I know its ancestor and the time at which speciation occured. These informations are stored in a data.frame, an example of which is here : PhyloTree