RE: Ontogentic shape comparison

Mon, 29 Oct 2012 00:54:17 -0700


----- Forwarded message from Javier Santos -----

Date: Fri, 26 Oct 2012 08:14:23 -0400
From: Javier Santos
Reply-To: Javier Santos
Subject: RE: Ontogentic shape comparison
To: Morphmet

Hello Carmelo,
 
I think I was too focused on the PCA graphs. Both the methods you mention are useful for what I was thinking about, although I prefer the images of MorphoJ over those of the older tps series. Thanks for the response!
 
 
Cheers,
Javier Santos
 
> From: [email protected]
> To: [email protected]
> Subject: Re: Ontogentic shape comparison
> Date: Thu, 25 Oct 2012 13:05:45 -0700
>
>
> ----- Forwarded message from Carmelo Fruciano -----
>
> Date: Thu, 25 Oct 2012 10:07:57 -0400
> From: Carmelo Fruciano
> Reply-To: Carmelo Fruciano
> Subject: Re: Ontogentic shape comparison
> To: [email protected]
>
> [email protected] ha scritto:
>
> >
> > ----- Forwarded message from "SANTOS SANTOS, JAVIER" -----
> >
> > Date: Wed, 24 Oct 2012 12:43:23 -0400
> > From: "SANTOS SANTOS, JAVIER"
> > Reply-To: "SANTOS SANTOS, JAVIER"
> > Subject: Ontogentic shape comparison
> > To: [email protected]
> >
> > Hello morphometricians,
> >
> > I am comparing ontogenetic shapes in two species of Lake Victoria
> > cichlids in MorphoJ (2D). I want to compare shape differences at each
> > ontogenetic stage. My question lies in what would be the better option
> > to compare the shapes visually (so for a illustration), and I would
> > like to know which of these two options you think is best to do so:
> > (1) Do a PCA in MorphoJ for each species at a given ontogenetic stage.
> > Then compare the consensus configuration for each. Or (2) Do the same
> > PCA and then compare both shapes at a determined scale factor (i.e.
> > 0.1). Or (3) Do a combined PCA and then compare the shapes obtained
> > with a negative scale factor (where one species is located) and with a
> > positive scale factor (where the other species is located).
> > Thanks in advance for your advice.
> >
>
> Dear Javier,
> I'm not sure I understand. Do you want to plot at each stage the
> difference between the two species as a shape change?
> You could do a Generalized Procustes Analysis of everything together,
> then compute mean Procustes residuals for each stage of each species
> and finally produce deformation grids between pairs of interest (for
> example in tpsSplin, if I remember).
> Another way to do it could be, after the GPA, just use the
> discriminant function routine in the program to get the graph for the
> difference in mean shape between the relevant pairs.
>
> If you, instead, use the PCA module in the program you will get, as
> far as I know, only shape changes associated with a certain PCA while,
> as far as I can tell, you wanna plot shape changes between species
> spanning all the dimensions (not only the first PC).
> I hope this helps,
> Carmelo
>
> --
> Carmelo Fruciano
> Post-doc - University of Konstanz - Konstanz, Germany
> Honorary Fellow - University of Catania - Catania, Italy
> e-mail [email protected]
> http://www.fruciano.it/research/
>
> ----- End forwarded message -----
>


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