-------- Original Message --------
Subject: Re: MorphoJ problem: erroneous canonical coefficients?
Date: Mon, 5 Mar 2012 10:45:16 -0500
From: Louis Boell <lbo...@evolbio.mpg.de>
To: morphmet@morphometrics.org
Hi Chris, hi Phillip,
thanks to both of you for the interesting and helpful comments. I can
confirm what Philipp says concerning multiple groups. Just for fun I
digitized the lollipop graphs resulting from CVA in MorphoJ for 11
groups and the resulting "coefficients" matched very closely the
loadings from a PCA on the group means.
I find this somewhat counterintuitive in so far as CVA is supposed to
quantify distinctness, not just variation
between groups in general. Personally I find that the mismatch between
displayed shape changes and coefficients proper can be
confusing/misleading, because both features result from the same
analysis which is supposed to address distinctness (analogous to
phenotypic FSTs). What, if not this distinctness, do the shape changes
in MorphoJ CVA reflect?
Best regards,
Louis
----- Ursprüngliche Mail -----
Von: "morphmet" <morphmet_modera...@morphometrics.org>
An: "morphmet" <morphmet@morphometrics.org>
Gesendet: Montag, 5. März 2012 16:14:07
Betreff: Re: MorphoJ problem: erroneous canonical coefficients?
-------- Original Message --------
Subject: Re: MorphoJ problem: erroneous canonical coefficients?
Date: Mon, 5 Mar 2012 06:01:43 -0500
From: Philipp Mitteröcker <mitte...@univie.ac.at>
To: morphmet@morphometrics.org
This is an interesting issue raised by Chris. In a recent paper, we
explained why shape changes corresponding to CVs should be visualized
based on the CV coefficients, just as for PCA. They are vectors in
tangent space. For two groups, the regression approach advocated by
Chris leads to a visualization of the group mean difference vector, not
the CV.
I am aware that this is a controversial topic and I am happy to discuss it!
Mitteroecker P, Bookstein FL (2011) Classification, linear
discrimination, and the visualization of selection gradients in modern
morphometrics. Evolutionary Biology 38, 100-114
Best wishes,
Philipp
Am 04.03.2012 um 15:56 schrieb morphmet:
-------- Original Message --------
Subject: Re: MorphoJ problem: erroneous canonical coefficients?
Date: Wed, 29 Feb 2012 06:38:43 -0500
From: Chris Klingenberg <c...@manchester.ac.uk>
Reply-To: c...@manchester.ac.uk
Organization: University of Manchester
To: morphmet@morphometrics.org
Dear Louis
There is nothing erroneous with the canonical coefficients provided by
MorphoJ, as far as I know.
The way you phrase your query suggests that you expect that the shape
changes associated with canonical variates (CVs) are just a scaled
version of the CV coefficients, as it holds for principal components.
This expectation is mistaken, because it misses the crucial difference
that CVs are not computed in shape (tangent) space itself, but in a
transformed space.
This problem has been extensively discussed in geometric morphometrics.
The computations of shape changes associated with CVs that are used in
MorphoJ are based on the solution proposed by Rohlf et al. (1996):
Rohlf, F. J., A. Loy, and M. Corti. 1996. Morphometric analysis of Old
World Talpidae (Mammalia, Insectivora) unsing partial-warp scores. Syst.
Biol. 45:344–362.
More discussion on transformed spaces and discriminant/canonical variate
analysis can be found here:
Klingenberg, C. P., and L. R. Monteiro. 2005. Distances and directions
in multidimensional shape spaces: implications for morphometric
applications. Syst. Biol. 54:678–688.
I hope this is useful.
Best wishes,
Chris
On 2/27/2012 5:23 PM, morphmet wrote:
-------- Original Message --------
Subject: MorphoJ problem: erroneous canonical coefficients?
Date: Thu, 23 Feb 2012 08:18:03 -0500
From: Louis Boell <lbo...@evolbio.mpg.de>
To: morphmet@morphometrics.org
Dear colleagues,
I am encountering a peculiar problem in MorphoJ: after performing CVA,
the Canonical Coefficients given in the results do not correspond at all
to the vector lengths in the lollipop shape change graphs. Either the
graphs or the Coefficients appear to be erroneous, because they
contradict each other. This only happens with CVA, not with PCA, for
which the results are nicely congruent. Did anyone else encounter this?
Any explanation?
Thanks for any help
Best regards,
Louis
--
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Christian Peter Klingenberg
Faculty of Life Sciences
The University of Manchester
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Telephone: +44 161 275 3899
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E-mail: c...@manchester.ac.uk
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___________________________________
Dr. Philipp Mitteroecker
Department of Theoretical Biology
University of Vienna
Althanstrasse 14
A-1090 Vienna, Austria
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email: philipp.mitteroec...@univie.ac.at
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