Changelog

Source: NEWS.md

MicrobiomeStat 1.4.4

New Features

• Added ref.level parameter to differential abundance testing functions for specifying reference group:

  • generate_taxa_test_single(): Single time point differential abundance testing
  • generate_taxa_test_pair(): Paired/longitudinal differential abundance testing
  • generate_taxa_trend_test_long(): Longitudinal trend testing
  • generate_taxa_change_test_pair(): Change score analysis between time points

• The ref.level parameter allows users to specify which group level should be used as the reference for comparisons, instead of relying on alphabetical ordering (first level alphabetically). This provides more flexibility and control over the statistical comparisons.

• Example usage:

  # Set "Control" as reference instead of alphabetically first group
  
  test.list <- generate_taxa_test_single(
    data.obj = data.obj,
    group.var = "treatment",
    ref.level = "Control",  # New parameter
    feature.level = c("Genus"),
    ...
  )

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MicrobiomeStat 1.4.3

Bug Fixes

• Fixed variable type handling in generate_taxa_test_single(): The function now correctly distinguishes between categorical (factor/character) and continuous (numeric/integer) variables. Previously, all variables were unconditionally treated as categorical.

Documentation Improvements

• Updated roxygen documentation for generate_taxa_test_single():
  • Fixed @return description to accurately reflect actual output columns
  • Added comprehensive explanation of variable type handling (categorical vs continuous)
  • Added detailed statistical methods documentation
  • Clarified difference between LinDA (for count/proportion data) and linear models (for other data)

Code Quality

• Removed legacy code from generate_taxa_volcano_single():
  • Removed unused meta_tab variable extraction
  • Removed unused group_level and reference_level variable definitions
  • Code is now cleaner and more maintainable

Testing

• Verified continuous variable support in volcano plots
• All tests pass with both categorical and continuous variables

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MicrobiomeStat 1.4.2

Bug Fixes

• Fixed pseudocount imputation for taxa change analysis
• Fixed log fold change pseudocount bias in taxa change functions
• Fixed critical statistical issues in normalization and CLR transformation
• Fixed barplot/areaplot mean calculation

New Features

• Added linda2() function with experimental sample weighting support
• Exported linda2 function for external use

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MicrobiomeStat 1.4.1 and earlier

See git commit history for details.