Matt, Liam and Ted, many thanks for your suggestions!
I had previously discarded ANCOVA because I wasn't getting the right
results for data I had simulated. With your suggestions and my seconds
thoughts I realized I was forgetting about the possibility of interaction.
That was the reason of all confusion and weird estimates on simulated data.
Thank you very much.
Cheers, Renata
--
Renata Brandt
Departamento de Biologia - FFCLRP
Universidade de São Paulo
Ribeirão Preto - SP - Brasil
(16) 82039533
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On Wed, Dec 14, 2011 at 6:33 PM, Liam J. Revell <liam.rev...@umb.edu> wrote:
> Hi Renata.
>
> I agree with Ted - you should be able to fit an ANCOVA model with
> gls(y~x+ecomorph,...,**correlation=corBrownian(phy=**tree)), or something
> like this, where ecomorph is a factor.
>
> Alternatively, you could use the method we devised in Revell & Collar
> (2009; Evolution) in which we first reconstructed the discrete character on
> the tree (in your case, this would be ecomorph), and then we fit a model in
> which different covariance structure between our variables was permitted on
> different branches of the tree. This method is also implemented in my
> phytools package (function: evol.vcv).
>
> All the best, Liam
>
> --
> Liam J. Revell
> University of Massachusetts Boston
> web:
> http://faculty.umb.edu/liam.**revell/<http://faculty.umb.edu/liam.revell/>
> email: liam.rev...@umb.edu
> blog: http://phytools.blogspot.com
>
>
> On 12/14/2011 3:26 PM, Theodore Garland Jr wrote:
>
>> Why not just include an interaction term between your main effect coding
>> variable (presumably coded as 0, 1 to indicate your two ecomorphs) and one
>> or more of your continuous independent variables?
>>
>> Cheers,
>> Ted
>>
>> Theodore Garland, Jr.
>> Professor
>> Department of Biology
>> University of California, Riverside
>> Riverside, CA 92521
>> Office Phone: (951) 827-3524
>> Home Phone: (951) 328-0820
>> Facsimile: (951) 827-4286 = Dept. office (not confidential)
>> Email: tgarl...@ucr.edu
>> http://www.biology.ucr.edu/**people/faculty/Garland.html<http://www.biology.ucr.edu/people/faculty/Garland.html>
>>
>> Experimental Evolution: Concepts, Methods, and Applications of Selection
>> Experiments
>> Edited by Theodore Garland, Jr. and Michael R. Rose
>> http://www.ucpress.edu/book.**php?isbn=9780520261808<http://www.ucpress.edu/book.php?isbn=9780520261808>
>> (PDFs of chapters are available from me or from the individual authors)
>>
>> ______________________________**__________
>> From: r-sig-phylo-bounces@r-project.**org<r-sig-phylo-boun...@r-project.org>[
>> r-sig-phylo-bounces@r-**project.org <r-sig-phylo-boun...@r-project.org>]
>> on behalf of Matt Pennell [mwpenn...@gmail.com]
>> Sent: Wednesday, December 14, 2011 12:17 PM
>> To: Renata Brandt
>> Cc: r-sig-phylo@r-project.org
>> Subject: Re: [R-sig-phylo] split data set and topology on PGLS
>>
>> Hi Renata,
>>
>> This seems to be an appropriate approach. (I am sure someone will correct
>> me if i am wrong in this). Phylogenetic regression in the way that you are
>> using it is basically to remove the statistical non-independence between
>> data points. Effectively what you are doing by splitting your data into
>> two
>> morphologies is pruning your tree. Under Brownian motion, evolution along
>> any branch is independent of evolution along any other branch, so pruning
>> your tree will not change the correlation struction of the data.
>> (Similarily you can still do PGLS with incomplete sampling of species). So
>> as long as you can justify splitting the data up as you are, it seems
>> fine.
>>
>> cheers,
>> matt
>>
>> On Wed, Dec 14, 2011 at 12:09 PM, Renata Brandt<renata.bra...@gmail.com**
>> >wrote:
>>
>> Hello everybody.
>>>
>>> I have some questions for you.
>>> When performing a phylogenetic regression between two continuous traits,
>>> the dependent trait clearly divides my data set in two distinct
>>> morphologies. This division overlaps with what I previously thought were
>>> two different ecomorphs. The relationship between the same traits seems
>>> to
>>> be different for each morphology.
>>>
>>> Now my question is:
>>> - Is it ok to split the data set (one data table and topology for each
>>> ecomorph) and reanalyze data to get the relationship between traits for
>>> each group? (That is what I would do if not using a phylogenetic
>>> approach).
>>> - If this is wrong, any hints on how should I proceed?
>>>
>>> Many thanks. Cheers.
>>>
>>> --
>>> Renata Brandt
>>> Departamento de Biologia - FFCLRP
>>> Universidade de São Paulo
>>> Brasil
>>> (16) 82039533
>>>
>>> /..)
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>>> R-sig-phylo@r-project.org
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>>>
>>>
>>>
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>>
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