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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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Deprecate MARGIN param #587

Closed Daenarys8 closed 2 days ago

Daenarys8 commented 2 weeks ago

The is PR references #578 and contains the following changes: 1- MARGIN parameter is deprecated in the following methods:

2- MARGIN parameter is removed from agglomerateByVariable and replaced with by 3- tests and examples are updated with param byin place of MARGIN 4- param docs is updated to show by default as ("rows", "cols")

Overall, by type i.e 1, 2, "rows", "features" etc. is maintained within method logic.

codecov[bot] commented 2 weeks ago

Codecov Report

Attention: Patch coverage is 69.31818% with 27 lines in your changes missing coverage. Please review.

Please upload report for BASE (devel@6dab0d7). Learn more about missing BASE report.

:exclamation: Current head 278909b differs from pull request most recent head 0f510fc

Please upload reports for the commit 0f510fc to get more accurate results.

Files Patch % Lines
R/deprecate.R 0.00% 16 Missing :warning:
R/splitOn.R 67.85% 9 Missing :warning:
R/getCrossAssociation.R 87.50% 1 Missing :warning:
R/utils.R 92.85% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #587 +/- ## ======================================== Coverage ? 67.38% ======================================== Files ? 41 Lines ? 4930 Branches ? 0 ======================================== Hits ? 3322 Misses ? 1608 Partials ? 0 ```

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TuomasBorman commented 2 days ago

Can you check that OMA and mia* packages will be updated?