Re: [MORPHMET] 2B PLS question

[Mike Collyer]

Angela,

The question I believe you are asking is if there is a way to have 2B-PLS work 
for n-dimensional data (n rows in your data matrix) when you have a 
s-dimensional phylogenetic covariance matrix (s x s dimensions for s species 
covariances) and s < n.  The phylo-integration function will work if you find a 
way to generalize your s x s species covariance matrix to an n x n specimen 
covariance matrix.  The n x n matrix would be certainly singular (if that is a 
concern) but not pose any computational hindrance on the phylo,integration 
function.

Doing this is not trivial.  Every cell of the n x n matrix would have to 
correspond to the species-species match in the s x s matrix.

There might also be a solution that involves centering specimen vectors, based 
on fitted values for a PGLS model with just a mean (i.e., phylo-mean-centering) 
and using standard 2B-PLS (without a covariance matrix input).

I offer these possible solutions as something one CAN do but do not wish to 
suggest this is something one SHOULD do.  I think this is sailing into 
unchartered waters with respect to statistical properties.

Cheers!
Mike

> On Jan 9, 2018, at 3:19 PM, Pena, Angela  wrote:
> 
> I am interested in using integration methods such as 2B-PLS on 3DGM data from 
> 4 different taxa with intraspecific variation. I was able to successfully run 
> 2B-PLS in geomorph considering all data points as independent. But I am 
> wondering if there is a way to consider that my taxonomic groups might be 
> following different patterns of integration. I know you can use the 
> phylo.integration function in geomorph for this, but this summarizes each 
> group to a species mean, and I am interested in the intraspecific variation. 
> Is there another way to do this without summarizing each group to a mean? Any 
> help would be greatly appreciated!
> 
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[MORPHMET] Re: Evolutionary allometry: theory and practice

[krisrhodes]

Hi Ariella,

If you aren't familiar with it yet, I recommend Zelditch's "Green Book", 
aka Geometric Morphometrics for Biologists: A Primer (2nd edition). It 
includes a chapter on allometric analysis and some practical examples, as 
well as references to many papers that apply the methods. 

Best,
Kristopher

On Monday, January 8, 2018 at 12:17:36 PM UTC-6, Ariella Rink wrote:
>
> Hi All
>
>
> I am a PhD student working on quantifying the importance of sexual 
> selection in contributing to diversification in South African monkey 
> beetles (Coleoptera: Scarabaeidae). An important component of my study 
> depends on investigating the allometric scaling relationships of hind leg 
> size and shape across populations of *Scelophysa trimeni*, taking the 
> phylogeny into consideration. Male monkey beetles use their hind legs in 
> battles over females. From my understanding of the literature that I have 
> read, this would be a study of evolutionary allometry, and would require 
> specialised analyses, such as Phylogenetic Generalised Least Squares 
> Regression in order to quantify the evolutionary allometric 
> slope/intercept, and compare and contrast the allometric slopes/intercepts 
> of each population. I do not have a strong background in evolutionary 
> biology; however, I am learning as I go. Consequently, I feel that I am 
> missing some important and basic aspects in my readings of the literature, 
> and would like to know if anyone could recommend to me material that 
> clearly lays out the theory of evolutionary allometry, as well as its 
> practical application.
>
>
> Kind regards
>
> Ariella Rink
>

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[MORPHMET] 2B PLS question

[Pena, Angela]

I am interested in using integration methods such as 2B-PLS on 3DGM data
from 4 different taxa with intraspecific variation. I was able to
successfully run 2B-PLS in geomorph considering all data points as
independent. But I am wondering if there is a way to consider that my
taxonomic groups might be following different patterns of integration. I
know you can use the phylo.integration function in geomorph for this, but
this summarizes each group to a species mean, and I am interested in the
intraspecific variation. Is there another way to do this without
summarizing each group to a mean? Any help would be greatly appreciated!

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