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
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
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