When to collapse (the data, not yourself)

[Nicholas_Bokulich]

Sweet plots @devonorourke!

@devonorourke

this got me wondering whether this kind of post-hoc collapsing was the appropriate way to analyze trends

I would personally avoid clustering on the front or back end. If you do it at either end, do it on the front and risk losing important information... but let the model tell you that! It is certainly interesting to test whether you receive similar (or more?) predictive power with taxonomy-collapsed features compared to ASVs.

@devonorourke

collapsing to Genus-level ahead of time can (and likely will) discard many instances in which unique species of insects with shared Genus are lumped together; this would further obscure the data

@devonorourke

keeping things at the ASV-level can lead to instances in which two ASVs differ between Sites, or Dates, and yet those ASVs are essentially the same sequence with perhaps a single nucleotide variant across the ~180 bp amplicon of interest

But that variation could be important. I'd say it's troublesome if you suspect these are the exact same species and exact same individual insects but multiple copy # variation is making these slight variants covary almost perfectly (e.g., those culex ASVs), but that is not really troublesome at all from the standpoint of these models... just for interpreting whether you really have 3 or 4 distinct culex species/subpopulations or if these are all one in the same.