Add Peak Detection and Deconvolution #36
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Skills updates
…o deconvolution
- Created documentation for `find_ftir_peaks` to detail peak finding in FTIR spectra. - Added `fit_peaks` documentation to explain peak fitting methods and parameters. - Introduced `fit_peak_df` for converting fitted peak objects to data frames. - Documented `get_fit_method` and `get_fit_spectra` for retrieving fitting details. - Added `plot_components`, `plot_fit_ftir_peaks`, and `plot_fit_residuals` for visualizing peak fitting results. - Included French translations for all documentation entries to support bilingual users.
Renames several peak-fitting helper functions to internal-style names (prefixed with `.`) and updates call sites, tightens `method` validation in `fit_peaks()` with `rlang::arg_match()`, and refreshes roxygen tags/parameter docs. Test coverage is updated to match fitted peak expectations, add validation for even `sg_n_norm`, and make plot-label assertions less brittle.
… fn calls, standardize cli errors, add @inheritParams for call param
pbulsink
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Jul 18, 2026
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Pull request overview
Adds peak detection, peak fitting (deconvolution), and related plotting utilities to PlotFTIR, bringing in peak-shape EM optimizers and a comprehensive test suite to support qualitative peak analysis workflows.
Changes:
- Introduces
find_ftir_peaks(),fit_peaks(),fit_peak_df(), and plotting helpers for fitted sums, residuals, and components. - Adds internal peak-shape EM optimization implementations and supporting helpers.
- Updates package exports/imports, documentation (Rd), and development/config files (lintr/ignores/skills/NEWS).
Reviewed changes
Copilot reviewed 14 out of 29 changed files in this pull request and generated 10 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/testthat/test-peak-fit.R | Adds extensive tests for peak finding, fitting, plotting, and EM optimizer behavior. |
| R/utils.R | Adds .process_language() helper and adjusts printing formatting. |
| R/PlotFTIR-package.R | Adds tibble::as_tibble import for new tibble-based outputs. |
| R/peak-fit.R | New peak detection/fitting/plotting implementation and embedded EM optimizer code. |
| R/aaa-shared_params.R | Extends shared roxygen params to include fitted_peaks. |
| NEWS.md | Documents new peak fitting feature addition. |
| NAMESPACE | Exports new public API functions and imports tibble::as_tibble. |
| man/read_ftir.Rd | Fixes Rd link target for utils::read.csv(). |
| man/read_ftir_directory.Rd | Fixes Rd link target for utils::read.csv(). |
| man/PlotFTIR-package.Rd | Updates package-level author metadata output. |
| man/plot_fit_residuals.Rd | Adds generated documentation for residual plotting. |
| man/plot_fit_ftir_peaks.Rd | Adds generated documentation for fitted-peak plotting. |
| man/plot_components.Rd | Adds generated documentation for component plotting. |
| man/optimization.Rd | Adds generated documentation topic for EM optimization helpers. |
| man/fit_peaks.Rd | Adds generated documentation for fit_peaks(). |
| man/fit_peak_df.Rd | Adds generated documentation for fit_peak_df(). |
| man/find_ftir_peaks.Rd | Adds generated documentation for find_ftir_peaks(). |
| man/dot-shared-params.Rd | Regenerates shared-params Rd with new parameter. |
| man/dot-process_language.Rd | Adds generated documentation for .process_language(). |
| man/dot-get_fit_spectra.Rd | Adds generated documentation for .get_fit_spectra(). |
| man/dot-get_fit_method.Rd | Adds generated documentation for .get_fit_method(). |
| DESCRIPTION | Adds dependencies needed by new functionality and tooling metadata. |
| .Rbuildignore | Tightens ignore patterns and adds additional ignored files. |
| .lintr | Adds lintr configuration. |
| .gitignore | Ignores additional local/dev artifacts. |
| .github/skills/tdd-workflow/SKILL.md | Updates testing workflow guidance. |
| .github/skills/r-code/SKILL.md | Updates R coding guidance (validation/deps/check expectations). |
| .github/skills/implement-issue/SKILL.md | Updates issue-implementation workflow guidance. |
| .github/skills/document/SKILL.md | Updates documentation workflow guidance. |
Files not reviewed (14)
- man/PlotFTIR-package.Rd: Generated file
- man/dot-get_fit_method.Rd: Generated file
- man/dot-get_fit_spectra.Rd: Generated file
- man/dot-process_language.Rd: Generated file
- man/dot-shared-params.Rd: Generated file
- man/find_ftir_peaks.Rd: Generated file
- man/fit_peak_df.Rd: Generated file
- man/fit_peaks.Rd: Generated file
- man/optimization.Rd: Generated file
- man/plot_components.Rd: Generated file
- man/plot_fit_ftir_peaks.Rd: Generated file
- man/plot_fit_residuals.Rd: Generated file
- man/read_ftir.Rd: Generated file
- man/read_ftir_directory.Rd: Generated file
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Adds explicit `signal` dependency checks in peak detection, preserves validated `ftir` objects across peak-fit plotting helpers, and fixes auto-peak argument forwarding in `fit_peaks()` via `do.call()`. It also removes `tibble::as_tibble()` usage from `fit_peak_df()` and cleans up package imports accordingly. Additional updates tighten `.process_language()` handling for `NULL`/empty inputs and make peak-fit tests call internal EM helpers explicitly through `PlotFTIR:::`.
pbulsink
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This PR merges the peak-fit.R file (and associated tests) from FTIRtools, an unpublished companion package. It permits users to detect and fit peaks using a variety of peak shapes, and plit fitted/residual curves. These techniques are used often in qualitative work.