Apologies for the delay in replying to your question.

Yes, you are still testing the covariation of the dependent variable(s) with the independent variable(s). For the pooled within-group regression, this test uses the within-group variation. That means that differences in the group means of the dependent and independent variables are removed from the analyses. In other words, the test is asking whether the individual deviations of the dependent variable(s) from their respective group means covary with the individual deviations of the independent variable(s) from their respective group means.

In my (possibly biased) view, the most accessible reference with further information on this is the following paper: Klingenberg, C. P. 2016. Size, shape, and form: concepts of allometry in geometric morphometrics. Development Genes and Evolution: 226: 113–137.
(Open access.)

I hope this helps.

Best wishes,

On 01/12/2017 12:03, EvoMorpho_16 wrote:
Dear friends,

It is getting hard to me to interpret the outcome of Pooled within regression in MorphoJ. 
I understand that the aim of this analysis is to remove the effect of "group" 
when studying covariation, but it is hard to understand the outcome: what am I testing 
with the p-value that it gives to me? Am I still testing covariation of x on y? Or I am 
testing differences in slopes of groups? Thanks beforehand

Some bibliography would be most wellcome

Christian Peter Klingenberg
School of Biological Sciences
University of Manchester
Michael Smith Building
Oxford Road
Manchester M13 9PT
United Kingdom

Web site:http://www.flywings.org.uk
Phone: +44 161 2753899
Skype: chris_klingenberg

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