specProc processes and analyzes emission spectra, streamlining the pipeline from raw spectra to calibrated concentrations. While specifically developed for laser-induced breakdown spectroscopy (LIBS), it seamlessly supports other plasma techniques such as ICP-OES. Select functions can also be used to process Raman and infrared spectroscopy data. The package structures data with one spectrum per row and wavelengths as column names, leveraging a C++ backend to power heavy computations.
# install.packages("remotes")
remotes::install_github("ChristianGoueguel/specProc", build_vignettes = TRUE)A C++ compiler is needed to build the package from source (Rtools on Windows, Xcode Command Line Tools on macOS).
The vignettes follow a typical LIBS analysis, on the
forageLIBS spectra of forage samples:
vignette("peak-fitting")): line identification, wavelength
calibration, line profiles and overlapping lines.vignette("preprocessing")): baseline correction,
normalization and other step_*() functions, in a tidymodels
workflow.vignette("calibration")): univariate curves, limits of
detection and quantification, and the net analyte signal of multivariate
models.vignette("plasma-diagnostics")): electron density,
temperature, LTE, self-absorption and calibration-free LIBS.They are also available as articles on the package website.
| Task | Functions |
|---|---|
| Line identification | libs_lines(), plot_lines(),
line_finder() (Shiny app),
wavelength_calibration(),
apply_calibration() |
| Line fitting | peak_fit(), multipeak_fit(),
plot_fit(), line_intensities(),
voigt_profile(), pseudo_voigt_profile(),
gaussian_profile(), lorentzian_profile(),
voigt_fwhm() |
| Preprocessing | baseline_arpls(), baseline_als(),
baseline_lsp(), snv(), msc(),
emsc(), normalize(),
savitzky_golay(), wavelet_features(),
reject_shots(), average() |
| Recipe steps | step_baseline(), step_snv(),
step_msc(), step_emsc(),
step_spectral_norm(), step_line_ratio(),
step_savgol(), step_wavelet(),
step_line_intensities(), step_reject_shots(),
step_opls(), step_o2pls(),
step_epo(), step_glsw(), and more |
| Orthogonalization | osc(), direct_osc(),
projected_osc(), opls(), o2pls(),
epo(), glsw(),
y_gradient_glsw() |
| Calibration | calibration_curve(), plot_calibration(),
nas(), pds() |
| Plasma diagnostics | saturation_summary(), electron_density(),
boltzmann_plot(), saha_boltzmann_plot(),
plot_boltzmann(), mcwhirter_criterion(),
self_absorption(), correct_self_absorption(),
cf_libs(), nist_lines(),
starkb_lines() |
| Outliers and robust PCA | robpca(), rospca(),
macropca(), cellpca(),
plot_outlier_map(), plot_cell_map(),
q_residuals(), dmodx(),
plot_influence(), hotelling_t2() |
| Robust statistics | summary_stats(), biweight_location(),
biweight_scale(), rousseeuw_croux(),
umad(), adjusted_boxplot(),
robust_bcyj() |
| Visualization | plot_spectra(), plot_embedding(),
plot_loadings(), plot_contributions() |
See the reference for the full list.
MIT © Christian L. Goueguel