structural zeros with two grouping levels

[anya-mueller]

Hello Huang,

Thank you for taking the time to look at my question.

I am running ancombc2 to find differentially abundant taxa between two groups. In the documentation for the function it says to only use the "group" argument if you have more than two levels, but structural zeros can only be detected if the group argument is not NULL.

When I run ancombc2 with group = NULL and struc_zero = FALSE the differential abundance of taxa with 0 abundance in one group is still modelled. Based on my reading of other posts about structural zeros I am under the impression that ancombc2 can't deal with those cases, so I am wondering if I should trust those models, or just look at the model results for which the abundance of a taxa in both groups is greater than zero. If I set group = "group_variable" and struc_zero = TRUE the taxa with zero abundance in one group are not modeled, though it seems I should not be doing this based on the function documentation since my grouping variable only has two levels.

Succinctly put: should I trust my model results for a taxa if it was not present in one group? Can I set group = "grouping_variable" and struc_zero = TRUE if my grouping variable only has two levels?

Thank you for your help.

Cheers,
Anya