Add explanation for agglomerateByPrevalence

microbiome / mia

Microbiome analysis

https://microbiome.github.io/mia/

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Add explanation for agglomerateByPrevalence #509

Closed thpralas closed 5 months ago

thpralas commented 5 months ago

This PR aims to solve the issue (https://github.com/microbiome/mia/issues/407) by making the function agglomerateByPrevalence easier to understand :

Specify the returned value
Add details on the way the function works
Clarify the examples

TuomasBorman commented 5 months ago

Very nice. I think we could still move it under agglomerate-methods with agglomerateByRank and agglomerateByVariable

I think this is more "agglomeration" than "prevalence" function, so that would be the best place for it

TuomasBorman commented 5 months ago

If you check the man page of agglomerate-methods, it does not describe detection and prevalence and as_relative parameters. (They are passed through with ...). You could add to agglomerate.R file those parameters under ... parameter.

" Passed to getPrevalence and getPrevalentTaxa functions. Used in agglomeratebyPrev function..." (Along with the current text.

As agglomerate.R already has ... parameter, you cannot ... above agglomerateByPrevalence function (otherwise it overwrites the one in agglomerate.R).

TuomasBorman commented 5 months ago

See the man page. You could modify description so that it describes the agglomeration functions in more general (it now only says about agglomerateByRank) --> Agglomeration functions can be used to sum-up to rank or variable or prevalence...