Thanks for this great tool! I have been successfully running Maaslin2 without issues.
I was wondering however if there is a way to account for ordered metadata in the model?
If I have ordered categorical metadata (for example weeks) is there a way to take that into account in the formula in Maaslin2? I have ordered the data in the metadata file and set a reference (first week) but it appears that it compares each week to the first (reference) week only, what I want to do is compare each week to the next week which in my scenario makes more biological sense then comparing to the reference (first) week.
For example is it possible to do forward or backward difference coding where the variable for a level is compared with the variable of the next or prior level.
Thanks in advance.