Tuomas Borman

@ake123 Can you have a look? Use the data from Slack --> add those taxonomy ranks that are provided in one of rowData's columns --> modify TAXONOMY_RANKS to support these...

How about if you drop "rank_lineage" column (it does not belong to these ranks) Check what is causing this issue. Seems that it's a problem that can be easily fixed....

Hi @ake123 Sorry for late reply. Your solution as such did not work (at least as I quickly tried it), but this seems to work ``` library("mia") data("GlobalPatterns") tse user...

This has been taken into account

I think this is not the best way to implement this. Better way is to keep those estimateDiversity.R and other files and just add estimateAlpha.R with estimateAlpha functionality (remove documentation...

> > Final comments. > > > > Lastly, run BiocCheck::BiocCheck() and fix warnings/notes related to this function (Check the mia.BiocCheck folder and the file inside it) > > The...

Ok, there was atleast some indentation problems (Bioc has a rule that indentation must be multiplication of 4 spaces) But these are easy and fast to fix, thanks!

At least the name should be addAlpha to follow new naming scheme (related to that we can have a discussion about naming, I will send you msg)

This looks good, the name should be addAlpha- And also it might be best to move deprecated functions to deprecate.R file

Also important to check that the code follows Biconductor guidelines. 1. BiocCheck::BiocCheck() 2. Fix issues related to these lines that are added by this PR (there are not many. I...