Organize parameter names v2

[Daenarys8]

Ping #579 .

[TuomasBorman]

Before I start review, is this duplicated with #562? What is the difference?

[TuomasBorman]

With quick look, everything seems ok, Can you still run BiocChec::BiocCheck() and ensure that lines that are modified in this PR follows Bioconductor guidelines? (If you did not do that already)

I will check this PR as soon as possible

[Daenarys8]

BiocChec::BiocCheck() has no errors and three warnings.
This PR re-did #562 because the latter's history was broken after rebase.

[codecov]

Codecov Report

Attention: Patch coverage is 81.02345% with 89 lines in your changes missing coverage. Please review.

Please upload report for BASE (devel@315beb0). Learn more about missing BASE report.

❗ Current head a22bd03 differs from pull request most recent head f01097f

Please upload reports for the commit f01097f to get more accurate results.

Files	Patch %	Lines
R/importMetaphlan.R	0.00%	13 Missing ⚠️
R/getCrossAssociation.R	89.58%	10 Missing ⚠️
R/importMothur.R	66.66%	8 Missing ⚠️
R/importQIIME2.R	71.42%	8 Missing ⚠️
R/calculateUnifrac.R	73.07%	7 Missing ⚠️
R/makeTreeSummarizedExperimentFromBiom.R	70.58%	5 Missing ⚠️
R/merge.R	44.44%	5 Missing ⚠️
R/taxonomy.R	76.19%	5 Missing ⚠️
R/getPrevalence.R	83.33%	4 Missing ⚠️
R/makeTreeSummarizedExperimentFromPhyloseq.R	71.42%	4 Missing ⚠️
... and 12 more

Additional details and impacted files

@@           Coverage Diff            @@
##             devel     #582   +/-   ##
========================================
  Coverage         ?   67.37%           
========================================
  Files            ?       41           
  Lines            ?     4928           
  Branches         ?        0           
========================================
  Hits             ?     3320           
  Misses           ?     1608           
  Partials         ?        0           

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[TuomasBorman]

BiocChec::BiocCheck() has no errors and three warnings. This PR re-did #562 because the latter's history was broken after rebase.

Thanks!

[TuomasBorman]

Ready for your review @antagomir

[TuomasBorman]

MARGIN issue will be fixed in different PR #578

[TuomasBorman]

Let's wait Leo's thoughts

[antagomir]

I might be missing something, is there a specific question or is this about general code review?

[TuomasBorman]

General code review. This is affecting the whole system so good to have second reviewer

[antagomir]

done

[TuomasBorman]

I ran the old unit tests, and found out that some old parameter names were removed. With these changes everything should be good

[TuomasBorman]

Ready!