deprecate f in favor of group

[Daenarys8]

ping #636

[codecov]

Codecov Report

Attention: Patch coverage is 79.50820% with 25 lines in your changes missing coverage. Please review.

Please upload report for BASE (devel@3f3b968). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
R/merge.R	64.10%	14 Missing ⚠️
R/calculateJSD.R	0.00%	3 Missing ⚠️
R/getPrevalence.R	80.00%	3 Missing ⚠️
R/splitOn.R	90.00%	3 Missing ⚠️
R/getDominant.R	87.50%	1 Missing ⚠️
R/utils.R	92.30%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff            @@
##             devel     #638   +/-   ##
========================================
  Coverage         ?   67.66%           
========================================
  Files            ?       44           
  Lines            ?     5362           
  Branches         ?        0           
========================================
  Hits             ?     3628           
  Misses           ?     1734           
  Partials         ?        0           

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[TuomasBorman]

Check comments. It seems that you have searched and replaced f with group.

[TuomasBorman]

• getDominant: group parameter for specifying the grouping used in merging. Merging is done before determining the dominant features. Agglomerating can be done for both taxonomy ranks (more common, agglomerateByRank() is utilized) or other variables (agglomerateByVariable() is utilized). (rank is deprecated)
• agglomerateByVariable: group parameter for specifying the grouping used in merging. Merging is meant to be done only for variables that are not taxonomy groups. (f is deprecated)
• splitOn: group parameter for specifying the grouping used in splitting. Splitting can be done for both taxonomy groups or other groups (more common). (f is deprecated)