NEWS

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panoramic 0.99.4

• Fixed local competition enrichment neighbor counts. closepairs() returns both orientations of a pair, and PANORAMIC now retains each pair once before adding it to the neighborhoods of its two endpoints.

• Added stat = "local_comp_global_enrichment" as an explicit alternative local-composition statistic. It uses a sample-wide target proportion (a random-label null conditional on observed locations), while the corrected edge-corrected CSR statistic remains the default.

• Fixed block-bootstrap handling: empty tiles no longer contribute artificial zero-valued block means, block-weighted estimates are invariant to point input order, and boot = "block" defaults to a 4-by-4 tile grid when tile counts are not supplied.

• Hardened input validation for sample identifiers, preparation parameters, and degenerate convex-hull windows.

• Build-system compatibility:

  • Switched the vignette to the knitr::knitr engine and added markdown to Suggests so R CMD build does not require Pandoc on Bioconductor builders.

• Documentation updates:

  • Updated DESCRIPTION, README.md, inst/CITATION, and the tutorial vignette to reflect the published Bioinformatics article (10.1093/bioinformatics/btag546) and current Bioconductor installation guidance.
  • Revised the package description to identify edge-corrected local competition enrichment as PANORAMIC's primary spatial statistic.
  • Removed generated help pages for non-exported implementation details so the installed manual exposes only the supported API.

panoramic 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.

panoramic 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.