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Subject: Re: How to demonstrate the power of geometric morphometrics?
Date: Thu, 31 Mar 2011 08:08:11 -0400
From: Carmelo Fruciano <[email protected]>
To: [email protected]
morphmet <[email protected]> ha scritto:
If
instead I show that I put in easy to understand variations, and the
process pulls out mixed modes of variation, then I will have more
trouble convincing people that the methods are useful.
So I wonder if the forum has any comments on these two: 1) I am
sure that forum readers have done something similar and analyzed
shapes of known variation to demonstrate/test the methods. Did your
PC’s represented the imposed variations well? Did they get all mixed
up like mine? If they get all mixed up, any recommendations on how to
convince people that geometric morphometrics is great?
2) How come one way of doing the analysis is finding PCs that match
what I put in whereas another way is finding mixed variations? My
guess is that it is because the variations are also changing centroid
size so the decomposition into PCs is mixing them up. If I had to bet
I would put my money on the way SHAPE and the code in R are doing the
scaling, but I have tried a few scalings and always end up with mixed
PCs in R. I am not suggesting that SHAPE is wrong. Differences could
also be because of differences in the distribution of the points on
the outline between SHAPE and my own implementation or in the rotation
of the axes in the PCA. Any comments?
Dear Ian,
I'm not sure that my consideration applies to your particular case,
but maybe using different ways of "normalizing" coefficients (to
eliminate size and orientation effects) can produce different results
(the same for normalizing in one case and not normalizing in another
case)...
About the general topic of "demonstrating the usefulness of geometric
morphometrics", I do think that the simple fact that you can easily
visualize results in terms of shape changes is an important
"demonstration" for people who are not used to GM methods.
Just my two cents
Carmelo
--
Carmelo Fruciano
Dipartimento di Biologia
University of Catania
Tel. +39 095 7306023
Cell. +39 349 5822831
e-mail [email protected]
http://www.fruciano.it/research/
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