Changes in version 2.1.1 (2026-02-13)                  

  - Replaced deprecated functions used by fast.Discrete() and in the
    vignettes.

                 Changes in version 2.1.0 (2024-12-14)                  

  - Added DBY() for discrete Benjamini-Yekutieli procedure.
  - If input p-values vector includes names, they are now included in
    the summary table generated by summary.DiscreteFDR(). For this to
    work with DiscreteTestResults class objects from package
    DiscreteTests, version 0.2.1 of that package is required.
  - Minor fix for wrong p-value CDF indices after selection. For the way
    they are used, this was inconsequential, but may have caused
    problems in the future.
  - Change order of output data: Data list is now output before Select
    list.
  - Fixed issues with Rcpp's rev() function in computations of adaptive
    DBH critical values.

                 Changes in version 2.0.1 (2024-10-24)                  

  - Introduction of mode parameter for hist() function to adapt
    construction of histograms in case of conditional p-value selection.
  - Remove amnesia dataset (moved to DiscreteDatasets package).
  - Function match.pvals() is no longer exported.
  - Performance improvement for step-up procedures, especially for large
    numbers of tests.

                 Changes in version 2.0.0 (2024-07-08)                  

  - New features:
      - discrete.BH(), DBH(), ADBH() and DBR() are now generic
        functions. The previously existing functionality is implemented
        in *.default methods.
      - discrete.BH(), DBH(), ADBH() and DBR() got *.DiscreteTestResults
        methods for processing DiscreteTestResults R6 class objects from
        package *.DiscreteTests directly, so they can be used within
        pipes.
      - For consistency of new generics and methods, the first parameter
        raw.pvalues needed to be renamed to test.results.
      - New parameter threshold for discrete.BH(), DBH(), ADBH() and
        DBR(). This enables selection of p-values which are smaller than
        or equal to a certain value. Note: observed p-values and their
        supports are then re-scaled, as the p-value distributions are
        now becoming conditional distributions. If no selection is
        performed (i.e. threshold = 1), print(), summary() and plot()
        outputs are as before. Otherwise, the now respect the re-scaled
        conditional distributions. Additionally, the DiscreteFDR S3
        class output objects of the functions discrete.BH(), DBH(),
        ADBH() and DBR() now include a list Select with values and
        information regarding selection.
      - New parameter pCDFlist.indices for discrete.BH(), DBH(), ADBH()
        and DBR(), which must have the same length as pCDFlist and may
        help increasing performance considerably. As pCDFlist can now
        include only unique supports, pCDFlist.indices must indicate the
        index of the p-values to which a given support belongs. If
        pCDFlist has the same length as test.results, it can be omitted
        (by setting it to NULL, the default). If users prefer using
        DiscreteTestResults objects, they do not have to take care of
        this, as unique supports and indices are automatically extracted
        from these objects.
  - New functions generate.pvalues() and direct.discrete.BH() as more
    flexible replacements for fisher.pvalues.support() and
    fast.discrete().
  - Step function evaluation in C++ code has been replaced by closely
    optimized inline functions which offer performance gains of 10-50%.

                 Changes in version 1.3.7 (2024-02-08)                  

  - Introduction of lifecycle mechanisms.
  - Marked fast.Discrete(), fisher.pvalues.support(), match.pvals(),
    kernel_*() and amnesia dataset as deprecated.
  - Various documentation updates.
  - Removal of links to discreteMTP packages, since it was removed from
    CRAN.

                 Changes in version 1.3.6 (2021-09-03)                  

  - Fixed a problem with fisher.pvalues.support that could cause
    p-values to be wrong or NA (Thanks to Iqraa Meah).
  - Added GitHub.

                 Changes in version 1.3.5 (2021-05-25)                  

  - Fixed a problem with fisher.pvalues.support that could cause an
    infinite loop when using alternative = two.sided (Thanks to Lukas
    Jansen).
  - Changed version scheme from x.y-z to x.y.z

                 Changes in version 1.3-4 (2020-02-14)                  

  - Added a NEWS.md file to track changes to the package.
  - Corrected a bug in plot.DiscreteFDR function that produced a false
    legend.
  - Added plausibility checks of arguments to discrete.BH and DBR
    functions.