Changes in version 0.2.5 (2026-09-12)                  

Breaking Changes

  - None.

New Features

  - None.

Enhancements

  - annotate_compounds() example now uses a user-provided library
    (lib_source = "user") instead of webchem, eliminating network
    dependency and ensuring stable CRAN checks.
  - Added pre-annotated example data
    (inst/extdata/annotated_example.rds) for use in
    filter_by_frequency() and save_postvocs_results() examples.
  - filter_by_frequency() and save_postvocs_results() examples now load
    pre-annotated data, avoiding repeated annotate_compounds() calls.
  - Added defensive checks for prop_df in annotate_compounds() to handle
    edge cases when pc_prop() returns unexpected results.

Bug Fixes

  - Fixed macOS CRAN check failure caused by webchem service
    unavailability in annotate_compounds() example.
  - Removed commented-out code lines from all examples per CRAN policy.

Documentation

  - Updated examples to be self-contained and executable without network
    access.
  - Added inst/extdata/annotated_example.rds as example data for
    downstream functions.

                        Changes in version 0.2.4                        

Bug Fixes

  - Removed all commented-out code lines from examples in
    batch_process_gcms(), extract_peak_areas(), and process_gcms_txt()
    per CRAN review. The previously commented examples are now
    uncommented and executable.

                        Changes in version 0.2.3                        

Bug Fixes

  - Replaced \dontrun{} with \donttest{} in all examples per CRAN
    policy.
  - Removed commented-out code lines from examples.
  - Removed default output paths from functions to comply with CRAN
    policies.

                        Changes in version 0.2.2                        

Bug Fixes

  - Removed redundant LICENSE file and simplified License field to GPL
    (>= 3) as requested by CRAN reviewer.

                        Changes in version 0.2.1                        

Bug Fixes

  - Fixed FileID matching in batch_process_gcms() to support exact
    filename mapping.

                        Changes in version 0.2.0                        

Breaking Changes

  - The extract_cas_abundance() alias has been removed. Please use
    extract_peak_areas() instead.
  - build_cas_abundance_matrix() has been renamed to
    build_cas_abundance() with simplified interface.

New Features

  - Added extract_peak_areas() as a more flexible replacement for
    extract_cas_abundance():
      - Supports data.frame input, file paths, and previous function
        outputs.
      - Can automatically detect and process all samples from a folder.
  - Added build_cas_abundance() as a replacement for
    build_cas_abundance_matrix():
      - Directly accepts output from extract_peak_areas().
      - No automatic file saving; returns a data.frame for user control.
  - Added save_postvocs_results() for unified saving of analysis
    results:
      - Supports CSV and XLSX formats.
      - Automatically adds single quote prefix to CAS columns to prevent
        Excel date conversion.
      - For XLSX output, multiple tables are saved as separate
        worksheets in one file.
  - Added filter_by_frequency() for two-step occurrence frequency
    screening:
      - Removes compounds detected in blank samples.
      - Filters by total frequency and treatment-specific frequency.
      - Returns detailed summary tables with flags for each compound.

Enhancements

  - annotate_compounds() now supports Excel input and automatically
    cleans CAS numbers.
  - filter_by_frequency() now accepts annotate_compounds() output
    directly.
  - save_postvocs_results() now checks whether a CAS column already has
    a leading single quote before adding one, avoiding duplication.
  - Improved documentation and examples for all functions.
  - CAS numbers are automatically cleaned (spaces removed) during
    parsing.

Bug Fixes

  - Improved handling of column name detection in extract_peak_areas().
  - Enhanced error messages for better user guidance.

Documentation

  - Added comprehensive README.md with workflow examples.
  - All functions now have complete roxygen2 documentation.
  - Added example data files (inst/extdata/txt/ with 13 sample .txt
    files and SampleID.xlsx) so all function examples are now
    self-contained and directly runnable.

                        Changes in version 0.1.0                        

  - Initial development version.
  - Basic package structure with core functions for GC-MS data
    processing.
  - Internal development only; not released on CRAN.