Changes in version 0.99.2                        

Documentation

  - Added \value sections (roxygen @return) to the
    MultiAssaySpatialExperiment class, combine, subset, and
    SpatialExperiment-coercion man pages, and to SpatialLayerList-class,
    documenting the values returned by the constructors, accessors,
    replacement, coercion, combining, and subsetting methods. Resolves
    the R CMD BiocCheck "missing \value" WARNING.

                       Changes in version 0.99.1                        

Bug fixes

  - readMERSCOPEMASE() and readCosMxMASE() now have runnable examples
    backed by minimal mock output directories bundled under
    inst/extdata/ (merscope_mock/, cosmx_mock/; generated by
    inst/scripts/make-example-mocks.R). This raises the share of
    exported-object man pages with runnable examples above the 80%
    BiocCheck threshold, resolving the R CMD BiocCheck ERROR.

                        Changes in version 0.9.6                        

Documentation

  - Reconciled the vignettes into a numbered, user-first set:
      - 1. Introduction to MultiAssaySpatialExperiment --- overview,
        anatomy, construction, accessors, subsetting, spatial
        operations, coercion, and a compact quick-reference table.
      - 2. Working with MultiAssaySpatialExperiment --- construction
        patterns, subsetting, spatial annotation and aggregation, and
        labels <-> shapes.
      - 3. MultiAssaySpatialExperiment use cases --- platform readers
        (Xenium, Visium, Visium HD, CosMx, MERSCOPE) and real-world
        spatial workflows.
  - Removed the Cheatsheet vignette (its chunks were globally
    unevaluated, which BiocCheck flags); its quick-reference content is
    now a table in the Introduction.
  - Applied Bioconductor vignette conventions: numbered
    VignetteIndexEntry, BiocStyle::doc_date() compiled dates, and
    structured author metadata.