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 <angiep...@gwu.edu> 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! > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > <http://www.morphometrics.org/> > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org > <mailto:morphmet+unsubscr...@morphometrics.org>. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.