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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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Deprecate taxonomyTree and addTaxonomyTree #496

Closed thpralas closed 7 months ago

thpralas commented 7 months ago

Replace taxonomyTree with getHierarchyTree and addTaxonomyTree with addTree.

Create new deprecate R script and manual page.

Create new get-values manual page.

antagomir commented 7 months ago

Some final things, sorry...

Is there a risk that addTree() gets mixed with other types of trees? Should it be addHierarchyTree(), or is it more generic so that you can use addTree for different things?

It is essential to update the OMA as well, or at least have a clear scheduled plan how that is done.

TuomasBorman commented 7 months ago

Actually it is now addHiearchyTree. It is just for adding calculated tree (not generic function for adding any kind of trees)

Updating OMA and other packages is taken into account. We have planned with @thpralas that names are changed everywhere immediately when PR in mia is merged

antagomir commented 7 months ago

Ah great! Then good to go I guess.