User Guide – Protocol Profiles

Protocol profiles bundle sensible defaults (preprocessing, validation, figure selection) for common scenarios. Use them with the CLI.

Profiles (examples)

• oil_basic: edible oil discrimination; reference-peak normalization; batch-aware validation; balanced accuracy + confusion matrix + top ratios + minimal panel.
• oil_heating: thermal stability; trend analysis (slopes/Spearman with FDR); stability ranking.
• oil_vs_chips: matrix effects; divergence metrics/effect sizes; oil-vs-chips plots.
• hsi_segment_roi: HSI segmentation (k-means) → ROI averaging → RQ; includes label maps and ROI spectra.

CLI usage with profiles

Use --protocol to point to a profile YAML or a named protocol installed via plugins.

# Oil discrimination profile
foodspec-run-protocol --input examples/data/oils.csv --protocol examples/protocols/oil_basic.yaml --auto --report-level standard

# Oil vs chips profile (harmonized multi-input)
foodspec-run-protocol \
  --input examples/data/oils.csv \
  --input examples/data/chips.csv \
  --protocol examples/protocols/oil_vs_chips.yaml \
  --auto --report-level full

- Figure selection profiles for publish: use foodspec-publish --profile {quicklook,qa,standard,publication}; quicklook = fewer figures, publication = richer set (or use --include-all-figures).

Report levels (CLI --report-level)

• summary: fewer figures (e.g., fig_limit ≈ 4)
• standard (default): typical figure set (e.g., fig_limit ≈ 8)
• full: include all figures (--include-all-figures)

See also: automation.md, cli_guide.md.