Re: [MORPHMET] Questions regarding correction for allometry & evolutionary allometry

2016-02-03 Thread Anneke van Heteren
Dear Nicole

In a recent paper of mine, I have also dealt with both allometry and
phylogeny, in a different way than Prof. Dean suggests. You might want to
have a look; it might give you some ideas. Here is the link:
http://link.springer.com/article/10.1007%2Fs13127-015-0238-2. Let me know
if you do not have access and I will send you a PDF.

Best wishes,

Anneke van Heteren

2016-02-02 19:26 GMT+11:00 Adams, Dean [EEOBS] <dcad...@iastate.edu>:

> Nicole,
>
>
>
> There is no need to perform multiple residual-based analyses. If you wish
> to obtain shape residuals where both the phylogeny and allometry (size)
> have been taken into account, these are found as residuals from the PGLS
> analysis: shape~size|phylogeny.
>
>
>
> However, a question then is what will these size/phylogeny shape residuals
> be used to investigate?  If the intention is to then evaluate these
> relative to some other factor (say groups), then the correct approach is
> just to perform a factorial PGLS analysis, where: shape~size+factor |
> phylogeny (shape is a function of size and some other factor, given the
> phylogeny). Additionally, if that factor describes groups, you may wish to
> include the size:group interaction term.
>
>
>
> In fact, if that is indeed the case, it is advisable NOT to perform the
> analysis in piecemeal fashion, where residuals from one regression are then
> used in a subsequent linear model to test other effects. The reason is that
> if there is some interaction between model effects (say, between size and
> groups), then the residuals from the first regression are not correctly
> capturing the observed patterns of variation.  This is the multivariate
> equivalent of the ANCOVA problem, and why an ANOVA on residuals from a
> regression is not always the same as performing the ANCOVA analysis. The
> best solution is to simply perform the factorial model, and account for
> size while examining other effects.  For this correct approach, one simply
> requires software that allows one to perform factorial PGLS. Geomorph (and
> as I recall, NTSYS) will allow uesrs to perform factorial PGLS.
>
>
>
> Hope this is helpful.
>
>
>
> Dean
>
>
>
> Dr. Dean C. Adams
>
> Professor
>
> Department of Ecology, Evolution, and Organismal Biology
>
>Department of Statistics
>
> Iowa State University
>
> www.public.iastate.edu/~dcadams/
>
> phone: 515-294-3834
>
>
>
> *From:* Nicole Dzenowski [mailto:ndzenow...@gmail.com]
> *Sent:* Monday, February 1, 2016 9:18 PM
> *To:* MORPHMET <morphmet@morphometrics.org>
> *Subject:* [MORPHMET] Questions regarding correction for allometry &
> evolutionary allometry
>
>
>
>
> Hi everyone,
>
>
>
> I had some questions regarding allometry correction. I'll be working with
> closely related specimens on a project where I think a moderate chunk of
> the shape variation is due to allometric size differences. Should (or can)
> I correct for both, as in, regress shape on size and take the residuals and
> then use a phylogenetic comparative method on those residuals and the size
> data and then do another multivariate regression and then use the residuals
> from that final regression as my new shape variables?
>
>
>
> Any help or direction is greatly appreciated.
>
>
>
> Thanks!
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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RE: [MORPHMET] Questions regarding correction for allometry & evolutionary allometry

2016-02-02 Thread Adams, Dean [EEOBS]
Nicole,

There is no need to perform multiple residual-based analyses. If you wish to 
obtain shape residuals where both the phylogeny and allometry (size) have been 
taken into account, these are found as residuals from the PGLS analysis: 
shape~size|phylogeny.

However, a question then is what will these size/phylogeny shape residuals be 
used to investigate?  If the intention is to then evaluate these relative to 
some other factor (say groups), then the correct approach is just to perform a 
factorial PGLS analysis, where: shape~size+factor | phylogeny (shape is a 
function of size and some other factor, given the phylogeny). Additionally, if 
that factor describes groups, you may wish to include the size:group 
interaction term.

In fact, if that is indeed the case, it is advisable NOT to perform the 
analysis in piecemeal fashion, where residuals from one regression are then 
used in a subsequent linear model to test other effects. The reason is that if 
there is some interaction between model effects (say, between size and groups), 
then the residuals from the first regression are not correctly capturing the 
observed patterns of variation.  This is the multivariate equivalent of the 
ANCOVA problem, and why an ANOVA on residuals from a regression is not always 
the same as performing the ANCOVA analysis. The best solution is to simply 
perform the factorial model, and account for size while examining other 
effects.  For this correct approach, one simply requires software that allows 
one to perform factorial PGLS. Geomorph (and as I recall, NTSYS) will allow 
uesrs to perform factorial PGLS.

Hope this is helpful.

Dean

Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
   Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/<http://www.public.iastate.edu/~dcadams/>
phone: 515-294-3834

From: Nicole Dzenowski [mailto:ndzenow...@gmail.com]
Sent: Monday, February 1, 2016 9:18 PM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] Questions regarding correction for allometry & evolutionary 
allometry


Hi everyone,

I had some questions regarding allometry correction. I'll be working with 
closely related specimens on a project where I think a moderate chunk of the 
shape variation is due to allometric size differences. Should (or can) I 
correct for both, as in, regress shape on size and take the residuals and then 
use a phylogenetic comparative method on those residuals and the size data and 
then do another multivariate regression and then use the residuals from that 
final regression as my new shape variables?

Any help or direction is greatly appreciated.

Thanks!
--
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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morphmet+unsubscr...@morphometrics.org<mailto:morphmet+unsubscr...@morphometrics.org>.

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[MORPHMET] Questions regarding correction for allometry & evolutionary allometry

2016-02-01 Thread Nicole Dzenowski

Hi everyone,

I had some questions regarding allometry correction. I'll be working with 
closely related specimens on a project where I think a moderate chunk of 
the shape variation is due to allometric size differences. Should (or can) 
I correct for both, as in, regress shape on size and take the residuals and 
then use a phylogenetic comparative method on those residuals and the size 
data and then do another multivariate regression and then use the residuals 
from that final regression as my new shape variables? 

Any help or direction is greatly appreciated.

Thanks!

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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You received this message because you are subscribed to the Google Groups 
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