Re: [MORPHMET] Ontogenetic changes in morphology

2015-02-18 Thread Anneke van Heteren
Dear Adeline Yong

Right now you are essentially plotting size (of the claw) against size (of
the crab). What you are interested in is shape against size. I am not sure
what program you are using now, but I would suggest MorphoJ, as it is quite
user friendly. You should do a multivariate regression of the Procrustes
coordinates onto size.You could then play around with different size
measures. (ln) centroid size of the object of interest is commonly used for
these types of analyses, but you could also try doing it with carapace size
and see if you get different results.
I hope that helps.

Best wishes,

Anneke van Heteren

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Re: [MORPHMET] MANOVA and shape data

2015-02-18 Thread Carmelo Fruciano

Dear all,
as an addendum to my previous message on tests for multivariate  
normality, I've just noticed that a new R package for this (MVN by  
Korkmaz et al 2014 -  
http://journal.r-project.org/archive/2014-2/korkmaz-goksuluk-zararsiz.pdf ) is  
out.

Best,
Carmelo

--
Carmelo Fruciano
Marie Curie Fellow - University of Konstanz - Konstanz, Germany
Honorary Fellow - University of Catania - Catania, Italy
e-mail c.fruci...@unict.it
http://www.fruciano.it/research/





Carmelo Fruciano c.fruci...@unict.it ha scritto:


Patrick Arnold patrick.arn...@uni-jena.de ha scritto:


Dear morphometrics,

I have two questions about applying MANOVA on shape data:

1. MANOVA assumes the data to be normal distributed. What is the  
best way to test normal distribution of multivariate shape data?  
And what is the best (free) software for this issue (is this  
embedded in PAST)?


Dear Patrick,
I normally use other software. However, it looks like PAST has some  
option for this at page 100 of the manual. On the other hand, you  
might want (also given the small sample sizes you mention below) to  
use resampling-based approaches...



2. The differences between my groups are very distinct in the CVA.


This is quite normal and well known (i.e. the fact that CVA shows  
often very clear separation of the groups). A detailed discussion of  
this can be found in


Mitteroecker, P. and F. Bookstein (2011). Linear Discrimination,  
Ordination, and the Visualization of Selection Gradients in Modern  
Morphometrics. Evolutionary Biology 38(1): 100-114.


Most importantly, Mitteroecker  Bookstein suggest using  
between-group principal component analysis as an alternative  
ordination technique. This is gaining popularity over time and, in  
my experience, it has been useful already in multiple cases  
(Franchini, Fruciano et al. 2014 - Molecular Ecology; Fruciano et  
al. 2014 - Biological Journal of the Linnean Society).


I want to test whether these differences are statistically  
significant, too. As my sample size only slightly exceeds the  
degrees of freedom, I want to apply the MANOVA onto the CVs (i.e.  
decrease in the number of dependent variables). Is this possible or  
is it redundant?


Although I have seen it done, I don't think this is a very good  
idea, as you have already suspected. Again, maybe resampling-based  
approaches might be a better choice (while, as Andrea Cardini was  
suggesting in some previous post, also recognizing the limitations  
of one's analysis).


I hope this helps,
Carmelo


--
Carmelo Fruciano
Marie Curie Fellow - University of Konstanz - Konstanz, Germany
Honorary Fellow - University of Catania - Catania, Italy
e-mail c.fruci...@unict.it
http://www.fruciano.it/research/





--
Carmelo Fruciano
Marie Curie Fellow - University of Konstanz - Konstanz, Germany
Honorary Fellow - University of Catania - Catania, Italy
e-mail c.fruci...@unict.it
http://www.fruciano.it/research/

--
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

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Re: [MORPHMET] Ontogenetic changes in morphology

2015-02-18 Thread Pere M. Parés-Casanova
You can also perform this analysis as a multivariate linear model (using
first variable, ln(CS) as independent variable) with PAST. Nervertheless,
number of Procrustes versus number of specimens can be a problem if you
sample size is not large enough.

Pere M.



On Dm, Febrer 18, 2015 09:06, Anneke van Heteren wrote:
 Dear Adeline Yong

 Right now you are essentially plotting size (of the claw) against size (of
 the crab). What you are interested in is shape against size. I am not sure
 what program you are using now, but I would suggest MorphoJ, as it is
 quite
 user friendly. You should do a multivariate regression of the Procrustes
 coordinates onto size.You could then play around with different size
 measures. (ln) centroid size of the object of interest is commonly used
 for
 these types of analyses, but you could also try doing it with carapace
 size
 and see if you get different results.
 I hope that helps.

 Best wishes,

 Anneke van Heteren

 --
 MORPHMET may be accessed via its webpage at http://www.morphometrics.org

 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org.



-- 
Pere M. Parés-Casanova PhD
Part-time Lecturer
Dep. of Animal Production
School of Agrifood and Forestry Science and Engineering
University of Lleida
Av. Rovira Roure 191
25198 Lleida (CATALUNYA, Spain)
Phone:+34973706460
Fax:  +34973702874
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