I agree with the suggestions so far. I just wanted to point out a few more alternatives:
You could use the geiger package to estimate the best scaling for the tworatetree transformation to do this (should be equivalent to the earlier solutions, though it would require running optimization). You could also use the OUwie package with a tree that has been given simmap mappings using phytools. The advantage of this is that you could evaluate Brownian models but you could also look at various Ornstein-Uhlenbeck models (though note that while there is information about different Brownian rates before and after a time slice, info about different alphas (strength of pull parameter) and thetas (the attractor, aka "optimal value") is rapidly (but not immediately) lost under an OU process). For completeness, especially for citations, note that O'Meara et al. (2006) and Thomas et al. (2006) independently arrived at essentially the same method, so it is worth reading both papers. Best, 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 Calendar: http://www.brianomeara.info/calendars/omeara On Mon, Sep 17, 2012 at 9:11 PM, Jason S <jas2...@yahoo.com> wrote: > > > Thanks, guys. That's exactly what I needed. > > > ________________________________ > From: Liam J. Revell <liam.rev...@umb.edu> > To: Matt Pennell <mwpenn...@gmail.com> > > -project.org> > Sent: Monday, September 17, 2012 9:22 PM > Subject: Re: [R-sig-phylo] variation in rates over time > > Hi Jason. Matt is absolutely correct. You can do this with phytools. > Say, for instance, you have an ultrametric phylogeny with branches in > millions of years (tree) and data vector containing the trait values for > species (x) and you want to test the hypothesis that the last 3.4 my has > a different rate of evolution than the rest of the tree, you could do > this as follows: > > library(phytools) # load phytools > tree<-make.era.map(tree,c(0,max(nodeHeights(tree))-3.4)) > plotSimmap(tree,pts=F,lwd=3) # visualize > fit<-brownie.lite(tree,x) # fit model > > That's it. Good luck. Liam > > Liam J. Revell, Assistant Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://phytools.blogspot.com > > On 9/17/2012 7:46 PM, Matt Pennell wrote: > > > 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 > > > > > > >> > >> > >> > 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 > > > [[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
