Changes in 1.24.4 (2026-09-26)
+ diff_dss_test() takes the methylation rates from the loci of bs that match
  diff_fit$gr, in that order. Before, it used every locus of bs, so a bs with
  more loci than the fit gave an error, and a bs with the same number of loci
  in another order gave rates for the wrong loci. It errors if bs is missing
  fit loci or has a different number of samples than diff_fit$design.

Changes in 1.24.3 (2026-09-25)
+ diff_binomial() used every sample in the pooled model under the null
  hypothesis, not only the samples in case and control. With other groups in
  group_column, the likelihood ratio statistic was wrong. Results with only
  the case and control samples are unchanged.

Changes in 1.24.2 (2026-09-25)
+ diff_methylsig() used the wrong log likelihood for the unmethylated reads
  when local information was used (local_window_size > 0): the term was
  missing the dispersion, lgamma((1 - mu) + 1e-100) instead of
  lgamma((1 - mu) * phi + 1e-100). This inflated the likelihood ratio
  statistic and gave many false positives. Results with
  local_window_size = 0 are unchanged.

Changes in 1.24.1 (2026-09-25)
+ diff_methylsig() drops every locus it can't test because of too few degrees
  of freedom. Before, only loci with df = 1 were dropped, and loci with df = 0,
  e.g. tiles with no coverage, were returned with NA results (issues #47 and
  #56).

Changes in 0.99.0 (2020-03-23)
+ Refactor functions and workflow from pre-0.99.0 releases
  o methylSigReadData() replaced with the functions:
    o bsseq::read.bismark()
    o filter_loci_by_coverage()
    o filter_loci_by_location()
  o methylSigTile() replaced with the functions:
    o tile_by_regions()
    o tile_by_windows()
  o Differential testing should be preceded with:
    o filter_loci_by_group_coverage()
  o binomialDiffCalc() is replaced by diff_binomial()
  o methylSigCalc() is replaced by diff_methylSig()
  o methylSigDSS() is replaced by diff_dss_fit() and diff_dss_test()
+ See "Using methylSig" vignette for full example.
+ See "Updating methylSig Code" vignette for how to retrofit pre-0.99.0 code.
