Suggestion to remove `na.action` argument from `runRDA`

microbiome / mia

Microbiome analysis

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

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Suggestion to remove `na.action` argument from `runRDA` #432

Open RiboRings opened 1 year ago

RiboRings commented 1 year ago

Hi!

What do you think about removing the na.action argument from runRDA and instead providing instructions in OMA how users can filter missing values themselves?

This could simplify the code of runRDA and prevent bugs due to differing dimensionality between tse and rda object.

antagomir commented 1 year ago

Sounds good to me at least. Should be fine when it is clear in the mia and OMA examples. Simplifying code is useful too.

TuomasBorman commented 12 months ago

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)

One option is to catch the na.action parameter and give more informal error message.

antagomir commented 1 month ago

@RiboRings could you check the status of this one, if we can handle & close the issue. This seems straightfwd.

RiboRings commented 1 month ago

Ok I'll have a look