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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