Leo Lahti

Great, thanks @adw96 - my intention was mainly to prepare for future developments in measurement technologies (as this class may be potentially long-living), rather than use this for the currently...

Perhaps to add example in OMA under subsection "Removing contaminated sequences" or something? Unless I am mistaken, this example is showing how to keep contaminated sequences only. Perhaps showing how...

How about providing an option to collapse the tree (default FALSE)? I assume that this is possible in many practical cases. And when it is not, the function could provide...

@TuomasBorman it seems to me that this has already been dealt with in the current updated methods?

Some literature refs on this aspect of ecological studies could be added in manpage reference list.

Also consider renaming mergeSEs -> combineSEs since now we are also using merge for row/col agglomeration.

Yes, if we are ok with having the output from splitBy as a list, rather than use `altExp`, `MAE`, or other such mechanism and their associated methods.

In principle, an entirely new package "MAEtools" would be useful for generic MAE manipulation.. but that's a whole other story again. Perhaps some others have interest to implement such thing...

This PR will be updated & reconsidered after #667 is ready. If we add the matrix completion step in vegan this would be require a new dependency, the "filling" package,...

Thanks for the feedback. We are making some final checks and I'm hoping to update & finalize this shortly now.