Tuomas Borman

> I implemented the requested changes and ran the biocCheck which didn't seem to have any issue with the new lines. The taxa have to be mapped back to the...

The indentation is still off. If there is juts couple lines that you are planning to change, you can create new PR and link this with that

Closing. The following PR will fix the issue https://github.com/microbiome/mia/pull/600

1. We do not have calculateDistance function. It was removed some time ago. (I think the function could be something to include) 2. Check if runRDA function (dbrda and significance...

Very nice, seems to work. However, let's first 1. check what parameters we have 2. Determine parameter names and descriptions 3. Modify documents and use inheritParam

This probably requires new PR since "everything" has changed. This has been in a plan of July

Closing, let's implement new PR soon

`mergeFeatureByRank`'s `agglomerateTree` seems not to agglomerate the tree but rather create a new one from the agglomerated `rowData` I think it should just drop those tips that are not present...

That would lead subset of TreeSE which is not the optimal case. Currently, the output of runRDA includes all the samples (samples with missing values are added to vegan::rda result)...

Encountering this issue again. Some rowData has superkingdom, and since it is not included in TAXONOMY_RANKS "superkingdom" taxonomy rank is not parsed. Not sure what is the most optimal solution,...