Changes in version 0.99.3                        

  - Major workflow/API restructuring:
      - Added panoramic_analyze() as the canonical end-to-end workflow.
      - panoramic() now delegates to panoramic_analyze() and returns a
        unified list with prep, stats, pooled, and tables.
      - Removed legacy compatibility arguments from the main wrappers
        (meta_model, tau2, group_method, keep_boot).
  - Replaced legacy two-stage group-comparison flow with multilevel
    modeling:
      - Retired/unexported panoramic_meta() and
        panoramic_compare_groups().
      - Added/exported panoramic_meta_mv() as the primary pooling API,
        including single-stage two-group contrasts (beta_diff, se_diff,
        z_diff, p_diff, fdr_diff) and optional group-specific
        heterogeneity estimates.
      - Contrast direction is now deterministic for grouped analyses.
  - Added new result access helpers:
      - panoramic_extract_contrast() for extracting spatialstats, meta,
        or contrast tables.
      - Pre-flattened tables are stored in
        metadata(se)$panoramic$tables.
  - Retired unused interpret/diagnostic helper prototypes
    (panoramic_sample_deviation(), panoramic_interpret_meta_mv()) from
    the public API to reduce surface area.
  - Expanded statistical and plotting functionality:
      - Refactored panoramic_spatialstats() internals for robustness
        (single-sample support, clearer per-sample/pair failure
        handling, and optimized local composition enrichment
        caching/bootstrapping).
      - L-function variance is computed via a delta-method transform
        from corresponding K-function estimates.
      - Added plot_representative_samples() and updated plot_volcano(),
        plot_forest(), and network plotting helpers to align with
        multilevel contrast outputs.
  - Documentation/submission updates:
      - Reworked vignette/tutorial to match the restructured workflow
        and current plotting APIs.
      - Added/updated man pages for newly exported functions and removed
        stale legacy docs.
      - Updated package metadata for Bioconductor review (Depends: R
        (>= 4.6), CITATION parsing fixes, .gitignore final newline).
  - Review-driven hardening and consistency fixes:
      - panoramic_prepare() now performs explicit schema validation
        (design$sample/design$group, duplicate sample IDs) and stronger
        coordinate/window checks after filtering.
      - Auto pair generation now uses observed marks (not unused factor
        levels), preventing inflated impossible pair sets under
        min_presence.
      - panoramic_meta_mv() now stops on ambiguous group labels after
        sanitization (make.names) to avoid silent group collisions.
      - panoramic_spatialstats() now degrades to per-sample NA outputs
        when local composition precompute fails, instead of aborting the
        full run.
      - create_spatial_network() now validates required rowData columns
        and documents/guards nonstandard sig_operator = "gt" behavior.
      - Plotting docs/messages now state the current two-group
        constraint (plot_forest(), plot_representative_samples()), and
        network man pages are synced to current function signatures.

                       Changes in version 0.99.0                        

  - First Bioconductor submission of PANORAMIC.
  - Added a full tutorial vignette showing how to prepare data, run
    pooled spatial analysis, and interpret results.
  - Improved plotting functions for differential colocalization
    summaries.
  - Added package citation metadata to make it easier to cite PANORAMIC
    and its associated preprint/release record.