Awesome, thank!
One remark: other key packages use “assay.type”, rather than “assay_type”. If it would be possible to use the same argument name this could support methods development and interlinking / argument passing.
Or if Maaslin3 internal conventions require using underscore on argument names, perhaps you could consider providing alias “assay.type” for the argument “assay_type”. This could be hidden by default but would do the same trick.