NRCan / PlotFTIR / 35339470905

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Build Type

push

github

Committed by web-flow

Commit Message

Add Raman spectra capabilities, closes #34 (#42)

* Add Raman spectra capabilities, closes #34

- 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

* Cleanup repo

* Testing & Validation

* Adding other raman data file formats and tests

* CMD Check requirements

* Improving Test Coverage

* Solving pkgdown complaints

* Apply suggestions from code review

* Resolving Copilot comments

* Fixed tests and checks.

* Updates to the FWHM algorithm.

* Additional raman-related tests & pkgdown update

* Updated Tests & Fixes

* Address PR review feedback for Raman capabilities

Fix correctness issues found in review of #42:

* Fix `sample_ids = NULL` crash caused by `is.na(NULL)` being tested
  before `is.null()`; extract the duplicated guard into the shared
  `.resolve_sample_ids()` helper.
* Reconcile `baseline_correct()`'s `lambda` default with its docs.
  `baseline::baseline.als()` treats lambda as a base-10 exponent, so the
  documented 1e6 smoothing penalty is `lambda = 6`, not 10.
* Whitelist `raman`/`normalized raman` in `smooth_spectra()` and
  `baseline_correct()` so FTIR data is rejected rather than silently
  Raman-processed.
* Make `plot_raman_stacked()`'s y-axis label bilingual.
* `read_raman_csv()` now reports true file line numbers, warns about
  malformed rows instead of dropping them silently, and parses single-#
  WiRE headers into `raman_metadata`.
* Set the `intensity` attr... (continued)

Coverage Stats

963 of 980 new or added lines in 8 files covered. (98.27%)

1 existing line in 1 file now uncovered.

3477 of 3512 relevant lines covered (99.0%)

121.97 hits per line