Add Raman spectra capabilities, closes #34

[pbulsink]

• Add read_raman() for RRUFF-style Raman data with ##FILETYPE=Raman headers
• Add plot_raman(), plot_raman_stacked() with non-reversed x-axis (increasing wavenumber)
• Add smooth_spectra() using signal::sgolayfilt() for Savitzky-Golay smoothing
• Add baseline_correct() using baseline::als() for Asymmetric Least Squares correction
• Add normalize_raman() for L2 vector norm and max intensity scaling
• Add find_peak_maxima() with optional FWHM computation
• Extend check_ftir_data() to accept 'raman' and 'normalized raman' intensity types
• Update DESCRIPTION, NAMESPACE, documentation, and add comprehensive test coverage

[Copilot]

Pull request overview

This PR adds first-class Raman support to PlotFTIR: new IO for Raman files, new Raman plotting functions, and a set of Raman-focused utilities (smoothing, baseline correction, normalization, peak finding), plus updates to validation, docs, and tests.

Changes:

• Add Raman readers/plotters: read_raman(), plot_raman(), plot_raman_stacked().
• Add Raman utilities: Savitzky–Golay smoothing, AsLS baseline correction, Raman normalization, and peak maxima detection (optionally FWHM).
• Extend core validation / IO paths and expand tests + generated documentation accordingly.

Reviewed changes

Copilot reviewed 19 out of 31 changed files in this pull request and generated 13 comments.

Show a summary per file

File	Description
tests/testthat/test-raman_utils.R	Adds test coverage for peak finding, smoothing, and baseline correction validation.
tests/testthat/test-plot_raman.R	Adds test coverage for Raman plotting behavior (axes, labels, stacked plotting).
tests/testthat/test-plot_ftir.R	Updates expected validation error strings to include intensity.
tests/testthat/test-maths.R	Updates tests to bilingual expectations and adds tests for Raman normalization.
tests/testthat/test-manipulations.R	Adds tests for band/marker behavior and internal transform helper.
tests/testthat/test-io.R	Adds extensive tests for Raman CSV parsing and JCAMP-DX Raman branch coverage.
R/utils.R	Extends check_ftir_data() to allow intensity column and Raman intensity types; extends intensity_type().
R/raman_utils.R	Introduces find_peak_maxima() implementation (with optional FWHM).
R/plot_raman.R	Introduces Raman plotting core + stacked + wrapper functions.
R/plot_ftir.R	Minor formatting adjustment in ggplot2 dependency error message.
R/maths.R	Adds normalize_raman() and updates baseline error handling to bilingual aborts.
R/manipulations.R	Adds smooth_spectra() and baseline_correct() implementations; fixes an error label in add_band().
R/io.R	Extends JCAMP-DX reader for Raman; adds read_raman() + CSV parser.
R/error_handling.R	Formatting-only changes to bilingual error/warn/inform helpers.
R/aaa-shared_params.R	Adds sample_ids to shared params (used by multiple new functions/docs).
NEWS.md	Adds a development bullet for Raman feature set (#34).
NAMESPACE	Exports newly added Raman functions/utilities; imports rlang .data.
man/smooth_spectra.Rd	Generated docs for smooth_spectra().
man/read_raman.Rd	Generated docs for read_raman().
man/plot_raman.Rd	Generated docs for plot_raman().
man/plot_raman_stacked.Rd	Generated docs for plot_raman_stacked().
man/plot_raman_core.Rd	Generated docs for internal plot_raman_core().
man/normalize_raman.Rd	Generated docs for normalize_raman().
man/find_peak_maxima.Rd	Generated docs for find_peak_maxima().
man/dot-shared-params.Rd	Generated shared-params Rd update for sample_ids.
man/dot-get_language.Rd	Generated docs for .get_language().
man/chemospec_to_plotftir.Rd	Minor generated Rd formatting update.
man/baseline_correct.Rd	Generated docs for baseline_correct().
DESCRIPTION	Adds baseline and signal to Suggests.
AGENTS.md	Updates repository overview to include Raman and new file structure.
.gitignore	Adds coverage.xml.

Files not reviewed (11)

• man/baseline_correct.Rd: Generated file
• man/chemospec_to_plotftir.Rd: Generated file
• man/dot-get_language.Rd: Generated file
• man/dot-shared-params.Rd: Generated file
• man/find_peak_maxima.Rd: Generated file
• man/normalize_raman.Rd: Generated file
• man/plot_raman.Rd: Generated file
• man/plot_raman_core.Rd: Generated file
• man/plot_raman_stacked.Rd: Generated file
• man/read_raman.Rd: Generated file
• man/smooth_spectra.Rd: Generated file

Suppressed comments (1)

R/manipulations.R:1216

• baseline_correct() documentation says the default lambda is 1e6, but the function default is lambda = 10, so user-facing docs and behavior disagree.

  ftir,
  sample_ids = NA,
  lambda = 10,
  p = 0.001

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