I used q2 composition ancombc2 in qiime-amplicon-2025.4. According to the corresponding publication (Lin and Peddada, 2024) there exist two versions of ancombc2: ANCOM-BC2 (no filter) and ANCOM-BC2 (SS filter). Which of these versions is implemented in q2 composition ancombc2, or does the --p-structural-zeros / --p-no-structural-zeros parameter switch between these two versions?
Our implementation of ancombc2 utilizes the version that does contain sensitivity analysis. Structural zeros can be passed in; this doesn't change the version of ancombc2 that's being used.
