Hi look also for motmot and auteur packages best
Paolo ________________________________________ Da: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] per conto di Matt Pennell [mwpenn...@gmail.com] Inviato: martedì 18 settembre 2012 1.46 A: Jason S Cc: R-sig-phylo@r-project.org Oggetto: Re: [R-sig-phylo] variation in rates over time Jason, I think the best way to do this is with the approach of O'Meara et al. 2006 Evolution "Brownie". Liam Revell has implemented this in R in his package phytools. You can modify the steps taken in this tutorial here http://phytools.blogspot.com/2011/07/running-brownielite-for-arbitrarily.html perhaps in conjunction with the function make.era.map() http://phytools.blogspot.com/2011/10/new-function-to-plot-eras-on-tree.html though I admittedly have not tried this myself. Perhaps Liam or someone else has a better explanation but I hope this is at least somewhat helpful. cheers, matt On Mon, Sep 17, 2012 at 7:33 PM, Jason S <jas2...@yahoo.com> wrote: > > > Hello, > > I see that there are several interesting alternatives to test for > different rates among clades. However, I was wondering if there is a method > to test for varying rates over time. I'm aware of Pagel's delta and the EB > model, but I was thinking more in terms of testing if there is a different > rate for the entire tree after a specified point in time. For instance, if > a snail predator colonizes an island 3.4 Mya, is there evidence for an > increased rate of evolution in the prey after that point in time? Something > like two lambdas, one for before and one for after that point in time. > > Thanks! > > Jason > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
