Leo Lahti

However I am not sure how to add such tests, in case this will be only included in OMA as an example. At least some quick manual tests to make...

If `calculateDistance` function is added back to mia, then rarefaction like here can be made optional part of that and tested properly.

Yes both things could be useful. Although I am not sure if it is worth wrapper if we could write `mia::runMDS()` instead of just `scater::runMDS(..., FUN=vegan::avgdist)`

@himmil when you have time you could check this, let's start with an OMA example, then consider if any new functionality (in mia) is really needed. Also good opportunity test...

Related to https://github.com/microbiome/OMA/issues/332

Perhaps need to open a separate issue about opening `calculateDistance` back to mia, and that should include the said rarefaction option (for counts)

Also be aware about the ready made rarification function that can be used https://github.com/microbiome/mia/pull/536

@Daenarys8 any chance to resolve the conflicts and finalize this one?

This is old PR, still open. What's the status of this one @Daenarys8 ?

Ok. I was just worried about having too many active open PRs.