Changes in version 2.0.0 (2026-02-19)                  

Major Changes (Physical-First Architecture)

  - [Core Logic] Shifted to a Physical-First landscape philosophy. The
    network layout now defaults to alpha = 0.75, giving 75% weight to
    physical protein composition to preserve biological specificity and
    sub-complex architecture.
  - [Interactive Layer] Replaced all static plotting functions
    (visualizeMapDirectLabels, visualizeMapWithLegend) with a
    high-performance interactive engine based on Cytoscape.js and Shiny.
  - [Visualization] Added explore() and runComplexMapApp() to launch the
    interactive viewer.
  - [S3 Object] Overhauled the print.ComplexMap method to provide a
    "Systems Biology Dashboard" highlighting Functional Diversity,
    Annotation Coverage, and Physical Density.
  - [Clustering] Updated functional clustering in generateNodeAttributes
    to use Average Linkage and a dynamic scaling factor to force
    functional diversity and prevent "monochromatic" maps.

Improvements

  - [Export] Enhanced toCytoscapeJSON with coordinate scaling and edge
    pruning to optimize browser performance for large networks.
  - [Export] exportNetwork now supports GraphML and sanitizes R-specific
    data types for Cytoscape Desktop compatibility.
  - [Documentation] Fully documented missing arguments (layout_seed,
    ...) and updated vignettes to reflect the v2.0 API.

Bug Fixes

  - [Metrics] Fixed a critical indexing error in evaluateComplexes where
    the Maximum Matching Ratio (MMR) would return NA when predicted and
    reference lists differed in size.
  - [CRAN] Eliminated non-ASCII characters in complexmap_S3.R and
    qcComplexList.R to ensure cross-platform portability.
  - [Architecture] Fixed a corrupt lazy-load database issue by ensuring
    consistent namespace exports.

                 Changes in version 1.1.2 (2026-02-11)                  

Added

  - [createComplexMap] Added ifRefineCpx parameter (default: FALSE).
    Step 1 (Complex Refinement) is now conditional, allowing users to
    process raw input lists without automatic merging.

Changed

  - [generateNodeAttributes] Enforced a strict 1:1 mapping between
    Primary Function and Node Color. Removed the weighted color blending
    logic to ensure visual consistency across the functional landscape.
  - [Logging] Updated verbose messaging to explicitly state refinement
    status during the workflow.

                 Changes in version 1.1.1 (2025-12-02)                  

Major Improvements

  - [Parallelism] Refactored evaluateComplexes to use future.apply
    instead of parallel::mclapply, enabling reliable multi-core
    computation on Windows.
  - [Workflow] Improved summarizeThemes() to accept add_to_object =
    TRUE, allowing theme metadata to be stored directly within the S3
    object.

Bug Fixes

  - [Dependencies] Moved clue from Suggests to Imports to ensure the
    Hungarian algorithm is always available for MMR calculation.
  - [UI] Fixed a runtime error in the interactive viewer when the
    color.by argument was null.
  - [Vignettes] Resolved build failures in vignette_02-workflow.Rmd
    caused by incorrect internal function calls.

                 Changes in version 1.1.0 (2025-11-15)                  

Added

  - [Benchmarking] Introduced benchmarkParameters() to systematically
    optimize mergeThreshold values against reference complexes.
  - [Metrics] Added dice and matching_score similarity options to
    refineComplexList.
  - [Quantitative] Added support for a color.by argument in
    visualization functions to map continuous experimental data to node
    colors.

Changed

  - [Defaults] Updated the default similarityMethod in refineComplexList
    to "matching_score".
  - [Traceability] refineComplexList now returns a mergeMap tibble for
    reproducibility.
  - [QC] Overhauled qcComplexList output to provide a formatted
    diagnostic report instead of raw R output.
  - [Terminology] Renamed the "overlap" similarity metric to "simpson"
    for scientific accuracy.

                 Changes in version 1.0.0 (2025-10-10)                  

  - Initial stable release.
  - Introduced the ComplexMap S3 object for structured proteomics
    workflows.
  - Added the high-level createComplexMap() wrapper.
  - Implemented core analysis suite: summarizeThemes(), queryMap(), and
    exportNetwork().
  - Released comprehensive documentation and three introductory
    vignettes.