Changes in version 0.99.20                       

  - The core carries its own trigamma(), so the solver no longer depends
    on R supplying one. Agrees with R's to 1.8e-15 across the range it
    is used over.

                       Changes in version 0.99.19                       

  - Declares its dependency on S4Vectors, which stashPACE() uses.

                       Changes in version 0.99.18                       

  - Condition signals build their messages without paste(), and the
    ridge check handles empty input directly rather than suppressing the
    warning it would raise.

                       Changes in version 0.99.17                       

  - New compactFit() drops the per-cell matrices before saving a fit,
    which the vignette previously did by assigning into a slot.
  - The vignettes read fits through accessors rather than @, which
    clears BiocCheck's note about slot access in examples and vignettes.

                       Changes in version 0.99.16                       

  - New stashPACE() copies a fit's readouts into metadata(spe), so
    results can travel with the data they came from. The solver state is
    not copied.

                       Changes in version 0.99.15                       

  - Records the Australian Government Research Training Program as
    funder in Authors@R.

                       Changes in version 0.99.14                       

  - PACEFit gains a validity method. Replacing a slot wholesale used to
    pass silently and break every readout downstream; fit@fit <- list()
    is now refused.
  - New accessors cellTypes(), paceParams() and fitState(), and
    validated replacement methods for neighbourSlopes(),
    varianceDecomposition() and topDrivers().

                       Changes in version 0.99.13                       

  - verbose = FALSE is now silent. The shrinkage step reported its
    progress regardless, because it never received the flag, and mashr
    printed its own on top of that.
  - Installation instructions use BiocManager::install().
  - The vignette evaluates every chunk.
  - Minimum R version is 4.6.0.

                       Changes in version 0.99.12                       

  - plotDecomposition() draws the zoom panel's percentage labels
    upright, so that neighbouring bars of similar height no longer
    overlap each other's text.

                       Changes in version 0.99.11                       

  - Added a canonical multivariate adaptive shrinkage implementation to
    the compiled core, alongside the existing mashr path. It reproduces
    mashr's calls exactly on both reference cohorts.

                       Changes in version 0.99.10                       

  - The driver score columns are named for what the method calls them:
    driver_score and driver_score_spec4, previously MCSD and MCSD4.
    plotDrivers() takes panels = "score" in place of "mcsd".

                       Changes in version 0.99.9                        

  - topDrivers() documents which model term each column holds. On a fit
    with a condition the table carries two different slopes, and they
    are not a raw and shrunken pair of the same quantity.
  - The condition vignette shows the responder decomposition and driver
    figures, and prints the driver table.

                       Changes in version 0.99.6                        

  - The per-pair gene score is called the driver score throughout the
    documentation and plot labels, matching the method description.

                       Changes in version 0.99.4                        

  - Fixed portability defects found by the Bioconductor build matrix:
    bit identity on arm64, a crash on Windows from static thread_local
    destructors, an unsupported system2(env=) on Windows, and missing
    -pthread on compile flags for Wasm.

                       Changes in version 0.99.0                        

  - Initial Bioconductor submission.