-------- Original Message --------
Subject: RE: Variance explained by size
Date: Mon, 29 Aug 2011 15:20:50 -0400
From: F. James Rohlf <[email protected]>
Reply-To: <[email protected]>
To: <[email protected]>
FYI: The option of appending ln(centroid size) to the shape variables is
also in tpsRelw but not yet in tprRegr.
-------------------
F. James Rohlf, John S. Toll Professor
Dept. Ecology & Evolution, Stony Brook University
Please consider the environment before printing this email
-----Original Message-----
From: morphmet [mailto:[email protected]]
Sent: Monday, August 29, 2011 2:24 PM
To: morphmet
Subject: Re: Variance explained by size
-------- Original Message --------
Subject: Re: Variance explained by size
Date: Mon, 29 Aug 2011 14:21:42 -0400
From: Dennis E. Slice <[email protected]>
To: [email protected]
Shape, by definition, already has isometric size taken out, though the ghost of
size may still be there via allometric components. If you want to examine
isometric+allometric components, then you are interested in form, not shape.
So,
1) SHAPE = f(CS)
2) FORM = f(CS)
The old Morpheus and all of the GRF programs allow you to restore size (form_i
= shape_i*cs_i).
There are cases where this is inadvisable. For instance, PCA, and Mitteroecker
et
al. (2004) recommend shape + log(CS) in some form as the appropriate data (see
their appendix for a good discussion of alternative formulations and
justifications). General extensions of this, called Procrustes size-shape space
analysis, are available in...well, they were in Morphologika. Probably in
MorphoJ, now, I would expect.
-ds
Mitteroecker, P, P Gunz, M Bernhard, K Schaefer, and FL Bookstein. 2004.
“Comparison of cranial ontogenetic trajectories among great apes and
humans.” JOURNAL OF HUMAN EVOLUTION 46 (6) (June): 679-697.
On 8/29/11 2:11 PM, morphmet wrote:
>
>
> -------- Original Message --------
> Subject: Re: Variance explained by size
> Date: Mon, 29 Aug 2011 14:06:09 -0400
> From: Guilherme Garcia <[email protected]>
> To: [email protected]
>
> hi,
>
> with respect to the question, you could simply use the R² of a
> multivariate regression over shape variables to get a % of shape
> variance explained by isometric variation (centroid size), and that
> (shape correlated with CS) would be allometric variation.
>
> but, if I wanted to have a measure of size variation (isometric +
> allometric) with respect to the total variation in the system, akin to
> the % of variation associated with a particular principal component,
> how would I proceed?
> more importantly, would this make any sense in a GM context?
>
> thanks in advance,
>
> guilherme.
>
> On Mon, Aug 29, 2011 at 12:44 PM, morphmet
> <[email protected]> wrote:
>>
>>
>> -------- Original Message --------
>> Subject: Re: Variance explained by size
>> Date: Mon, 29 Aug 2011 11:44:00 -0400
>> From: Dennis E. Slice <[email protected]>
>> To: morphmet <[email protected]>
>>
>> Without looking at the specific example, it may be worth mentioning
>> that there are two issues size/shape relationships - isometric and
>> allometric. GPA removes isometric size variation, but there could
>> still be an association with size and shape. For instance, maybe all
>> large specimens were tall, skinny rectangles while all small ones
>> were short, fat rectangles. Size could, in such a case, "explain" 100% of
"pure"
>> shape variation. -ds
>>
>> On 8/26/11 5:29 PM, brian boivin wrote:
>>>
>>> Hi,
>>> In Geometrics morphometrics for Biologist : A Primer (pg7) it
>>> says:"In the two species mentionned above (in which PC1 accounts for
>>> 99.4% of the variance), SIZE explains 71% of the variance in SHAPE
>>> in one species, but only 21.7% in the other."
>>> I did not find any information in the book to explains the impact of
>>> size on the variance in shape. Did I miss something?
>>> How can one calculate the % of variance in shape explained by size?
>>> Email:[email protected]
>>> Thank you for your time
>>> B.B
>>>
>>>
>>
>> --
>> Dennis E. Slice
>> Associate Professor
>> Dept. of Scientific Computing
>> Florida State University
>> Dirac Science Library
>> Tallahassee, FL 32306-4120
>> -
>> Guest Professor
>> Department of Anthropology
>> University of Vienna
>> -
>> Software worth having/learning/using...
>> Linux (Operating System: Ubuntu, CentOS, openSUSE, etc.) OpenOffice
>> (Office Suite: http://www.openoffice.org/) R package (Stats/Graphics
>> environment: http://www.r-project.org/) Eclipse (Java/C++/etc IDE:
>> http://www.eclipse.org/) Netbeans (Java/C++/etc IDE:
>> http://netbeans.org/) Zotero (FireFox bibliographic extension:
>> http://www.zotero.org/)
>> ========================================================
>>
>>
>>
>
>
>
--
Dennis E. Slice
Associate Professor
Dept. of Scientific Computing
Florida State University
Dirac Science Library
Tallahassee, FL 32306-4120
-
Guest Professor
Department of Anthropology
University of Vienna
-
Software worth having/learning/using...
Linux (Operating System: Ubuntu, CentOS, openSUSE, etc.)
OpenOffice (Office Suite: http://www.openoffice.org/)
R package (Stats/Graphics environment: http://www.r-project.org/)
Eclipse (Java/C++/etc IDE: http://www.eclipse.org/)
Netbeans (Java/C++/etc IDE: http://netbeans.org/)
Zotero (FireFox bibliographic extension: http://www.zotero.org/)
========================================================
