Changes in version 1.15.10                       

  - [Major] Name of the two arguments for lefser function is changed
    from groupCol and blockCol to classCol and subclassCol,
    respectively.
  - [Major] Defunct expr argument in lefser
  - [New function] lefserPlotFeat plots the histogram of relative
    abundance (in the (0,1) interval) of the selected features
  - [New function] lefserPlotClad draws the cladogram of the
    significantly more abundant taxa and their LDA scores
  - [New function] lefserClades runs the lefser, returning additional
    information (e.g., agglomerates the features abundance at different
    taxonomic ranks) required for lefserPlotClad.
  - [New feature] Visualization functions are using a color-blind
    friendly color palette by default.

                       Changes in version 1.15.7                        

  - [Major algorithm update] We remove the step (createUniqueValues) in
    the lefser function, which used to add small random numbers to make
    all the values unique. Potential issues (e.g., LDA) due to excess 0s
    should be managed by filtering out low abundant features from the
    input.

                       Changes in version 1.15.3                        

  - The column names of lefser output is changed to c("features",
    "scores") from c("Names", "scores")
  - [New feature] The get_terminal_nodes function to select only the
    terminal nodes of the hierarchical features (e.g., taxonomic data).
  - [Major algorithm update] Add an option for adjusting the first
    Kruskal-Wallis Rank Sum Test and Wilcoxon-Rank Sum test for multiple
    hypothesis testing through the new argument method in the lefser
    function.

                       Changes in version 1.14.0                        

  - [Error fix] The lefserPlot function merged the duplicated labels
    when the truncated name of the feature is used. Now those are
    plotted separately.
  - [New feature] The lefserPlot function accepts the title argument
    that adds the barplot title.
  - [Update] The feature names of the lefserPlot outputs are
    re-positioned for the improved readability.
  - [Major algorithm update] Sub-sampling and bootstrap for LDA step in
    the lefser function is removed. Now the LDA score is calculated
    directly from the whole samples.

                       Changes in version 1.12.0                        

Significant user-visible changes

  - The checkAbundances argument in lefser() checks that data are as
    relative abundances and warns if otherwise (@LiNk-NY @sdgamboa, #28)
  - relativeAb helper function available to convert data (@LiNk-NY)
  - Deprecate the expr argument and use relab (short for relative
    abundances)
  - Add group labels to lefserPlot (@LiNk-NY #25, @asyakhl #31)
  - 'Interoperating with phyloseq' section added to the vignette (#16)

                        Changes in version 1.0.0                        

  - lefser is an R/Bioconductor implementation of the LEfSe method for
    microbiome marker discovery
    (https://doi.org/10.1186/gb-2011-12-6-r60)
  - LEfSe uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and
    Linear Discriminant Analysis to find biomarkers in groups and
    sub-group blocks.
  - lefser also implements the format of the LEfSe barplot of results