I’m wondering if you have any thoughts on whether maaslin2 is appropriate for a 3x3 (or k x k) cross-over study design. While technically the design has repeated measurements of the microbiome where a mixed model might be appropriate, it doesn’t seem like we can account for sequence or period with this model. Would you agree? I wonder if there is a method that is more suited to the crossover design than a straightforward longitudinal design.
Interested in your thoughts.