Grouping variable for SECOM

[BKretzler]

This is both perhaps a feature request for SECOM as well as an attempt to discuss the best way to test my hypothesis with SECOM. I am wanting to use SECOM to test for correlation between microbes in the rhizosphere soil of 2-3 crop species growing within a single plot (i.e. in an intercropping arrangement). The experiment was set up in such a way that there are 3 crop species that have been grown in all possible 1, 2, and 3 species combinations (happy to provide more detail here if it's helpful).

My approach for now will be to subset my phyloseq object by crop and cropping combination and treat each crop as a distinct ecosystem with common samples. All this said, it would be helpful to be able to set a grouping variable for SECOM if at all possible to be able to test for differences in correlation based on specific treatments/categorical variables. If there is already a way to do this that's great! I just didn't see it in the documentation.