[R-sig-phylo] Estimating MRCA dates

Dan Rabosky drabosky at berkeley.edu
Thu Feb 2 16:55:32 CET 2012


Hi Brian-

It has been awhile since I played with chronopl(), but at the time, I convinced myself that results were substantially different from penalized likelihood as implemented in r8s. I haven't explored this exhaustively, but at the time, I was very much convinced that the results of chronopl were potentially problematic. Other folks have mentioned to me that they've observed similar differences between r8s and chronopl and that they've recovered bizarre smoothed trees from chronopl. Perhaps someone with more recent chronopl experience can weigh in on this...

~Dan



On Feb 2, 2012, at 6:06 AM, Brian O'Meara wrote:

> Ape can do this, function chronopl. In general, one good way to find out
> which package can do something is by looking at the task view for
> phylogenetics: http://cran.r-project.org/web/views/Phylogenetics.html .
> This will also allow you to install all the phylogenetics packages (at
> least those on CRAN) with just a couple of commands. An updated version
> should be coming out later today (and if someone notices other things
> missing, please let me know).
> 
> Brian
> 
> _______________________________________
> Brian O'Meara
> Assistant Professor
> Dept. of Ecology & Evolutionary Biology
> U. of Tennessee, Knoxville
> http://www.brianomeara.info
> 
> Students wanted: Applications due Dec. 15, annually
> Postdoc collaborators wanted: Check NIMBioS' website
> Funding wanted: Want to collaborate on a grant?
> 
>  



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