i have a dataset where I’m seeing low richness and high within group dispersion. I’d like to be able to test if these two things are corrected or not. I know permdisp is usually calculated on the PCoA, and Im wondering if anyone knows of implementations where its possible to adjust for alpha diversity?
As an update (thanks @Nicholas_Bokulich) for people who come later, what I ended up doing was exporting the distance matrix via the python API, calculated PCoA, and dropped the first PC (correlated with alpha diversity) and then used the same euqation as the skbio implementation. It did an okay job separating out the alpha effect, which I think worked