-------- Original Message --------
Subject: Re: modularity hypotheses for subsets of landmarks in a single
configuration
Date: Mon, 25 Jul 2011 17:01:48 -0400
From: Chris Klingenberg <[email protected]>
Reply-To: [email protected]
Organization: University of Manchester
To: [email protected]
Hello
Just to prevent any misconceptions, here are a few comments on what
MorphoJ does and does not do in relation to stuff in my 2009 paper in
Evolution & Development
http://www.flywings.org.uk/PDF%20files/EvolDev2009.pdf
For the modularity test, MorphoJ implements *only* the approach with a
single Procrustes fit, within one configuration. The reason for this is
that the comparison of the strength of covariation between different
subsets only really makes sense if the different parts that show up in a
subset are in a single configuration. Because the comparison is across
*different* subsets, it is sensible to treat all landmarks as part of
one configuration (otherwise, the same two landmarks would sometimes be
part of the same structure, sometimes not -- not a very consistent basis
for the comparison).
For two-block PLS, MorphoJ is now implementing *both* variants (since
version 1.03a -- 2 July of this year).
The option with two separate blocks examines covariation between parts
viewed as separate shapes (for instance the shape of the face versus the
shape of the braincase). Both parts are in separate datasets, and
therefore have undergone separate Procrustes fits. As a result, any
integration due to variation in the relative sizes and positions of the
parts is not considered.
The option of two blocks within a single configuration considers the
covariation between two sets of landmarks that are part of the same
shape. Some covariation can therefore stem from variation in the
relative arrangement and sizes of the two parts.
The MorphoJ implementations of both PLS versions come with the RV
coefficient as a measure of the strength of association between the two
sets of landmarks. As pointed out in the 2009 paper, these RV
coefficients can differ quite considerably.
I hope this clarifies things.
Best wishes,
Chris
On 7/25/2011 6:27 PM, morphmet wrote:
-------- Original Message --------
Subject: modularity hypotheses for subsets of landmarks in a single
configuration
Date: Sun, 24 Jul 2011 14:30:44 -0400
From: John Denton <[email protected]>
To: [email protected]
Hi all,
I am interested in tests using subsets within a single configuration,
especially for modularity hypotheses (sensu Klingenberg [2009]), and
comparing them to fits with two separate blocks. It appears that MorphoJ
does not yet implement modularity hypotheses for subsets within a single
configuration, and I am wondering if there is a package in R, or a script,
that is available for such an analysis that includes an allometric
correction before running.
Also, I am also working a bit with fluctuating asymmetry, and have a
question about its use with subsets in a single configuration--is the
problem with running modularity analyses on a subset of the asymmetric
component of a Procrustes ANOVA without reference to the total
configuration alleviated if the the modularity hypothesis is run assessing
subsets within the total configuration?
Lastly, I'm wondering about methods for assessing digitization error (the
error term in Procrustes ANOVA)--for example, is there a way to get these
results by looking at the contributions to a matrix correlation between
symmetric and asymmetric components by the diagonal and off-diagonal
entries, instead of digitizing all samples multiple times?
Thanks very much!
~John
--
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Christian Peter Klingenberg
Faculty of Life Sciences
The University of Manchester
Michael Smith Building
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Manchester M13 9PT
United Kingdom
Telephone: +44 161 275 3899
Fax: +44 161 275 5082
E-mail: [email protected]
Web: http://www.flywings.org.uk
Skype: chris_klingenberg
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