Felix Ernst

> What I do for these arrays, where x is the array is: BStringSet(as(as(as.raw(x),"XRaw"),"BString")) This will convert it to a character nonetheless instead of retaining the original integer value. In...

Yes, you are right. With the conversion the constructor is avoided, which either would call `as.character` (BStringSet) or would not work at all with integer values (BString). Nice! > -...

There also some other inconsistencies for showing the name of elements. The length of names seems to be treated differently. Probably a historic reason based on the positioning of the...

Any news on this effort?

Hmm OK. Thanks for the info. Bioconductor packages come with a certain badge of stability, which I am looking for.

>in case one's taxonomy ranks fall outside of what is hard-coded in mia::TAXONOMY_RANKS, it breaks functions like taxonomyRanks. I would phrase it the other way around like this: taxonomyRanks breaks...

> PS: I personally would leave the default TAXONOMY_RANKS as is, but move it to options(), so I can be (globally) modified by the user as needed. And if it...

Currently, I still don't see that this is a problem to be addressed in the `mia` package. 1. Your example includes a function named `agglomerate_by_rank`, which is not available from...

> when we assume that users in general know what they are doing in such cases? Well you spelled it out there. By experience, I have to assume that nobody...

It is not. Have a look at the code.