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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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Improve documentation #585

Open TuomasBorman opened 2 weeks ago

TuomasBorman commented 2 weeks ago

After we moved similar functions under same manual page, we lost some "hidden" parameters that were described under .... That is because one manual page can have only one description for each parameter, i.e., if we have documentation coming from multiple R files, descriptions of ... parameters are not merged; the documentation has only one description of ....

--> Check these problems. If this kind of issue is found, ensure that all the documentation can be found from manual page (merge descriptions manually to single R file).

For instance, agglomeration functions are under single "agglomeration" manual page. However, it seems that agg.na.rm parameter is missing from [here](https://microbiome.github.io/mia/reference/agglomerate-methods.html even though it is listed here

artur-sannikov commented 2 weeks ago

I'd also probably split at least agglomerateByRank and agglomerateByPrevalence functions in separate pages, as for example, detection and prevalence parameters are not required for agglomerateByRank (?).

TuomasBorman commented 2 weeks ago

The idea was to harmonize the naming and documentation so that it is intuitive for user that these agglomerate* function do similar things. We cannot avoid having documentation pages which include parameters that are not shared with every function in the page; they are very common. But this is something that we can discuss what is the best way to organize the manual. Updating manuals was already in task list.