postvocs 0.2.6

New Features

filter_by_frequency() gains a new argument remove_blank_compounds (default FALSE).
- When FALSE, blank samples are excluded from frequency calculations, but compounds detected in blanks are retained. A new flag column In_Blank ("*" if detected in any blank sample, otherwise empty) is added to abundance, round1, round2, and summary_table. Blank sample columns are retained in abundance (placed before the frequency columns).
- When TRUE, compounds detected in any blank sample are removed from all samples. summary_table keeps the Removed_in_Blank column ("-" for removed compounds) and computes their frequencies (overall and within each group) from the original data, excluding blank samples from the denominator. No In_Blank column is added in this mode.

summary_table in filter_by_frequency() no longer contains the Removed_in_Blank column when remove_blank_compounds = FALSE.
Blank and internal standard samples are always excluded from frequency calculations, regardless of remove_blank_compounds.

Updated filter_by_frequency() documentation to describe the new remove_blank_compounds argument, the In_Blank flag column, and the revised summary_table layout.

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. # postvocs 0.2.3

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.