----- Forwarded message from Javier Santos
<[email protected]> -----
Date: Fri, 7 Mar 2014
05:59:49 -0500
From: Javier Santos
<[email protected]>
Reply-To: Javier Santos
<[email protected]>
Subject: RE: Shape analysis without
removing size as a factor?
To: Morphmet
<[email protected]>
Hello Celena,
The Procrustes fit standardizes centroid size to unit = 1, which is not exactly the same as removing size as a factor from the shape data. If you have a large size range in your samples (for example in ontogenetic studies), to eliminate size before performing the PCA you first do a multivariate regression of shape on lnCS ,and then perform the PCA on the residuals from the regression. By using the residuals from the MANCOVA you are removing size variation from the shape data. You can do this in MorphoJ or any other GMM software. I hope this helps.
Best regards,
Javier Santos-Santos
[email protected]
PhD student
Integrative Biogeography and Global Change Group
- Museo Nacional de Ciencias Naturales (MNCN-CSIC)
http://www.ibiochange.mncn.csic.es/
Associated Researcher @ Evolutionary Morphology of Vertebrates Lab
- Universiteit Gent
http://www.fun-morph.ugent.be/
The Procrustes fit standardizes centroid size to unit = 1, which is not exactly the same as removing size as a factor from the shape data. If you have a large size range in your samples (for example in ontogenetic studies), to eliminate size before performing the PCA you first do a multivariate regression of shape on lnCS ,and then perform the PCA on the residuals from the regression. By using the residuals from the MANCOVA you are removing size variation from the shape data. You can do this in MorphoJ or any other GMM software. I hope this helps.
Best regards,
Javier Santos-Santos
[email protected]
PhD student
Integrative Biogeography and Global Change Group
- Museo Nacional de Ciencias Naturales (MNCN-CSIC)
http://www.ibiochange.mncn.csic.es/
Associated Researcher @ Evolutionary Morphology of Vertebrates Lab
- Universiteit Gent
http://www.fun-morph.ugent.be/
>
From: [email protected]
> To: [email protected]
> Subject: Shape analysis without removing size as a factor?
> Date: Tue, 4 Mar 2014 22:05:55 -0800
>
>
> ----- Forwarded message from [email protected] -----
>
> Date: Fri, 31 Jan 2014 20:33:52 -0800
> From: [email protected]
> Reply-To: [email protected]
> Subject: Shape analysis without removing size as a factor?
> To: [email protected]
>
> ----- Forwarded message from Celena Toon <[email protected]> -----
>
> Date: Mon, 20 Jan 2014 15:36:52 -0500
> From: Celena Toon <[email protected]>
> Reply-To: Celena Toon <[email protected]>
> Subject: Shape analysis without removing size as a factor?
> To: [email protected]
>
> Hello,
>
> I've been working on my master's thesis that uses a geometric
> morphometric approach to analyzing the human tibia and the _expression_
> of sexual dimorphism. I've previously consulted this forum about
> formatting my text files and it has been a wonderful help! After
> conducting my analyses, I did not get the results expected and my
> advisor wants me to seek other ways I could potentially analyze my
> data to cover all my bases and make sure I'm not doing something
> wrong. Using MorphoJ, I conducted a Procrustes fit, a principal
> components analysis, and a discriminant function analysis. I know
> that the Procrustes fit removes size as a factor, but is there a way I
> could analyze my data in terms of both size and shape? Or should I be
> approaching this differently?
>
> Thank you,
> CT
>
> ----- End forwarded message -----
>
> ----- End forwarded message -----
>
> To: [email protected]
> Subject: Shape analysis without removing size as a factor?
> Date: Tue, 4 Mar 2014 22:05:55 -0800
>
>
> ----- Forwarded message from [email protected] -----
>
> Date: Fri, 31 Jan 2014 20:33:52 -0800
> From: [email protected]
> Reply-To: [email protected]
> Subject: Shape analysis without removing size as a factor?
> To: [email protected]
>
> ----- Forwarded message from Celena Toon <[email protected]> -----
>
> Date: Mon, 20 Jan 2014 15:36:52 -0500
> From: Celena Toon <[email protected]>
> Reply-To: Celena Toon <[email protected]>
> Subject: Shape analysis without removing size as a factor?
> To: [email protected]
>
> Hello,
>
> I've been working on my master's thesis that uses a geometric
> morphometric approach to analyzing the human tibia and the _expression_
> of sexual dimorphism. I've previously consulted this forum about
> formatting my text files and it has been a wonderful help! After
> conducting my analyses, I did not get the results expected and my
> advisor wants me to seek other ways I could potentially analyze my
> data to cover all my bases and make sure I'm not doing something
> wrong. Using MorphoJ, I conducted a Procrustes fit, a principal
> components analysis, and a discriminant function analysis. I know
> that the Procrustes fit removes size as a factor, but is there a way I
> could analyze my data in terms of both size and shape? Or should I be
> approaching this differently?
>
> Thank you,
> CT
>
> ----- End forwarded message -----
>
> ----- End forwarded message -----
>
----- End forwarded message
-----
