That's a fairly small tree to be doing this with -- an old rule of thumb (I think from Pagel) is 20 tips per parameter. Common issues are zero length (or effectively zero length) branch lengths (what is min(phy$edge.length)?) and polytomies (methodologically not a problem, but many packages don't deal well with these).
Brian _______________________________________ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info/calendars/omeara On Tue, Sep 18, 2012 at 4:08 PM, Agus Camacho <[email protected]>wrote: > Dear all, I tried to test something similar to Jason, but relating the > change in rates to the acquisition of a trait, instead to a specific date. > > For that, I used a phylogeny with ten taxa, without outgroup. > I used exactly the same script gently proposed by Liam but got the > following error message: > "Error in solve.default(model1$hessian) :Lapack routine dgesv: system is > exactly singular" > > I've been looking through the internet but was not able to identify what > causes this error. Any hint about that? > > BTW, anybody knows how to directly answer a message found in the digest of > the mail list, without leaving the thread? > > Below, I pasted the complete thread dealing with this topic. > > Cheers, > Agus > > Message: 9 > Date: Tue, 18 Sep 2012 00:13:00 -0400 > From: "Brian O'Meara" <[email protected]> > To: Jason S <[email protected]> > Cc: "[email protected]" <[email protected]> > Subject: Re: [R-sig-phylo] variation in rates over time > Message-ID: > < > cakywhkq-jjroqzdvfutphi4xopxam+aaacu64nldb3inxoz...@mail.gmail.com> > Content-Type: text/plain > > 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 <[email protected]> wrote: > > > > > > > Thanks, guys. That's exactly what I needed. > > > > > > ________________________________ > > From: Liam J. Revell <[email protected]> > > To: Matt Pennell <[email protected]> > > > > -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: [email protected] > > 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 > > >> [email protected] > > >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > >> > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > R-sig-phylo mailing list > > > [email protected] > > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > R-sig-phylo mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > > > > [[alternative HTML version deleted]] > > > -- > Agustín Camacho Guerrero. > Doutorando em Zoologia. > Laboratório de Herpetologia, Departamento de Zoologia, Instituto de > Biociências, USP. > Rua do Matão, trav. 14, nº 321, Cidade Universitária, > São Paulo - SP, CEP: 05508-090, Brasil. > > [[alternative HTML version deleted]] > > > _______________________________________________ > R-sig-phylo mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > [[alternative HTML version deleted]]
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