NEWS

postvocs 0.2.5 (2026-09-12)

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.

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.

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

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.

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

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

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.

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.

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.

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.