Changes in version 0.99.1                        

  - ewas_regions() and ewas_blocks() are new and are now the interface
    most analyses need: each takes a SummarizedExperiment or
    GenomicRatioSet and returns a GRanges, running the whole analysis
    the corresponding pipeline stage runs, including the within-subject
    permutation null and subject-level selection stability that
    previously existed only in the stage drivers.
  - SummarizedExperiment, GenomicRanges, S4Vectors and IRanges moved
    from Suggests to Imports. The object interface is no longer
    optional.
  - Assay selection: NULL now means the assay named M, or the only
    assay. This is what a GenomicRatioSet needs, since minfi stores Beta
    first. A beta-valued assay is converted to M-values with a message
    rather than analysed with a warning.
  - Six numerical helpers (pinv(), demean_by_group(),
    demean_rows_by_group(), within_df(), fold_assign(), state_labels())
    are internal: they were pipeline plumbing rather than part of the
    interface. The pipeline's stage drivers now source their own copy of
    the core instead of loading the package.
  - NAMESPACE is generated by roxygen2 from @export and @importFrom
    tags, and roxygen Markdown is enabled, so help pages render links
    and code spans instead of raw Markdown.
  - The vignette starts from an object rather than a matrix, adds an
    installation section, shows how to build the input from 450K and
    EPIC minfi objects with combineArrays(), analyses a real 2,000-probe
    subset of GSE237561 that now ships in inst/extdata, and compares the
    package with bumphunter, DMRcate, ENmix, coMethDMR,
    minfi::blockFinder(), limma::duplicateCorrelation() and
    variancePartition::dream().
  - moderate_variance() no longer checks for limma with
    requireNamespace(); it is an Imports dependency.
  - URL and BugReports point at the package repository, where users
    report issues, rather than at the pipeline that generates the
    package.

                       Changes in version 0.99.0                        

  - First version, extracted from the ewas-crossarray-harmonise pipeline
    (bin/ewasml.R). Function bodies are unchanged from the pipeline
    source; the package adds documentation, a namespace and unit tests.