People, many thanks for keeping this list so functional. Sorry for the slow reply, had a small accident, but is ok now. I'll answer Liam first and Ted and Brian in sequence.
Liam, yes, the error is fatal, and the BrownieREML worked. But seems
it did not converged:
These are the results:
> brownieREML(tree,data[,"Area_Km2"],maxit=2000)$sig2.single
[1] 6.444619e+12
$logL1
[1] -135.4347
$sig2.multiple
2
4.911978e+12
$logL2
[1] -135.6168
$convergence
[1] FALSE
Also tried the Ouwie option, but then I needed to generate a
simmap.tree. Tried with make.simmap but the help tells me it only
works for discrete data, and my response variable is continuous. To be
more informative, I pasted below a very small graph of the uncorrected
relationship I want to analyze using phylogenetic methods.
Ted and Brian, thanks for you advice and references on number of species.
Im comparing nearly all known syntopic species of two sister clades with
different morphs. I know thats inappropriate for inferring adaptation and
for estimating several parameters from such a low number of species.
However, I expected to be able to reliably recover the differences between
the two groups and the degree to which phylogeny was explaining the
relationships.
However, for this case, as my data are highly heteroskedastic (see graph
below) and the differences between the treatments is related to the maximum
value that the response variable attains, do you think that adding a
outgroup and performing a Bartlets test over phylogenetic contrasts would
at least make a honest test of the relationship?
Agus
[image: Imágenes integradas 1]
2012/9/18 Theodore Garland Jr <theodore.garl...@ucr.edu>
> That number of 20 comes up from the simulations provided by both of these
> papers:
>
> Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for
> phylogenetic signal in comparative data: behavioral traits are more labile.
> Evolution 57:717-745.
>
> Freckleton, R. P., P. H. Harvey, and M. Pagel. 2002. Phylogenetic analysis
> and comparative data: a test and review of evidence. Am. Nat. 160:712-726.
>
> Note, however, that both of those sets of simulations assumed no
> measurement error in the phenotypic trait(s) and no error in the
> phylogenetic topology or branch lengths. Hence, they may well have
> underestimated how many species you need in the real world! As they say,
> your mileage may vary ...
>
> Cheers,
> Ted
>
> Theodore Garland, Jr.
> Professor
> Department of Biology
> University of California, Riverside
> Riverside, CA 92521
> Office Phone: (951) 827-3524
> Facsimile: (951) 827-4286 = Dept. office (not confidential)
> Email: tgarl...@ucr.edu
> http://www.biology.ucr.edu/people/faculty/Garland.html
> http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ
>
> Experimental Evolution: Concepts, Methods, and Applications of Selection
> Experiments. 2009.
> Edited by Theodore Garland, Jr. and Michael R. Rose
> http://www.ucpress.edu/book.php?isbn=9780520261808
> (PDFs of chapters are available from me or from the individual authors)
>
> ________________________________________
> From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org]
> on behalf of Brian O'Meara [bome...@utk.edu]
> Sent: Tuesday, September 18, 2012 1:25 PM
> To: Agus Camacho
> Cc: r-sig-phylo@r-project.org
> Subject: Re: [R-sig-phylo] variation in rates over time, unexpected
> message when using Brownie.lite
>
> 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 <agus.cama...@gmail.com
> >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" <bome...@utk.edu>
> > To: Jason S <jas2...@yahoo.com>
> > Cc: "R-sig-phylo@r-project.org" <R-sig-phylo@r-project.org>
> > 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 <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]]
> >
> >
> > --
> > 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
> > R-sig-phylo@r-project.org
> > 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.
<<Rplot02.png>>
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