Leo Lahti

@ake123 is this ready?

Can you close all issues that are ready?

One aspect in using TAXONOMY_RANKS is to enforce certain standards. However, there are situations where some other categories are needed for a similar purpose. We are now working on that...

This is good point. It would be great to see a comment from @FelixErnst on this but I know that it may take some time before he can respond. Should...

What would be an example of a case where customization option leads to problems, when we assume that users in general know what they are doing in such cases? I...

Sounds good to me at least. Should be fine when it is clear in the mia and OMA examples. Simplifying code is useful too.

If the other split function `splitBySomeOtherRanks` (with some other name) will be made, then `splitBy` could be potentially reserved exclusively for the case using the grouping factor `f`. It is...

Right, it was only in the discussion part so far. It is better to not mix those indeed, and I agree that `splitBy` is disturbingly similarly named with `splitByRanks` bc...

@RiboRings could you check the status of this one, if we can handle & close the issue. This seems straightfwd.

The issue #185 had discussion on including the full abundance table, optionally, as one of the outputs in `splitByRanks`, or a similar function. As well as about implementing something like...