Preprocessing Tools for Laser-Induced Breakdown Spectroscopy

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Documentation for package ‘specProc’ version 0.8.3

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A B C D E F G H I L M N O P Q R S T U V W Y Z

-- A --

adjusted_boxplot Adjusted Boxplot
apply_calibration Apply a Wavelength Calibration
average Fast Average for Large Spectral Dataset

-- B --

baseline_als Asymmetric Least Squares
baseline_arpls Asymmetrically Reweighted Penalized Least Squares
baseline_lambda Baseline Smoothness Parameter
baseline_lsp Least-Squares Polynomial
biweight_location Biweight Location
biweight_midcorrelation Biweight Midcorrelation
biweight_midcovariance Biweight Midcovariance
biweight_midvariance Biweight Midvariance
biweight_scale Biweight Scale
boltzmann Plasma Temperature from a Boltzmann Plot

-- C --

calibration_curve Univariate Calibration Curve
cellpca Robust PCA by Casewise and Cellwise Weighting (cellPCA)
center Data Centering
cf_libs Calibration-Free LIBS Quantification
contributions Q and T-squared Contributions of a PCA Model
correct_self_absorption Self-Absorption Correction with an Internal Reference Line
correlation Correlation Coefficients: Pearson, Spearman, Kendall, Chatterjee, and Biweight Midcorrelation

-- D --

directional_outlyingness Directional Outlyingness for Skewed Distribution
direct_orthogonal Direct Orthogonalization
direct_osc Direct Orthogonal Signal Correction
dmodx Distance to the Model (DModX) of a PCA Model

-- E --

electron_density Electron Density from Stark Broadening
emsc Extended Multiplicative Signal Correction
epo External Parameter Orthogonalization

-- F --

flagged_regions Flagged Regions of a MacroPCA or cellPCA Fit
forageLIBS LIBS Spectra of Forage Samples

-- G --

gaussian_profile Gaussian Function
generalized_boxplot Generalized Boxplot
glsw Generalized Least Squares Weighting
glsw_alpha Relative GLSW Weighting Parameter

-- H --

hotelling_t2 Hotelling's T-squared Statistic of Samples in an Embedding

-- I --

iqr_outliers Interquartile Range Method

-- L --

libs_lines Candidate Emission Lines for LIBS Spectra
line_finder Interactive Identification of Emission Lines
line_intensities Intensities of Emission Lines
loading_peaks Peaks of the Loadings of a PCA
lorentzian_profile Lorentzian Function

-- M --

macropca Robust PCA for Cellwise and Casewise Outliers (MacroPCA)
mcwhirter_criterion McWhirter Criterion for Local Thermodynamic Equilibrium
medcouple_weight Medcouple Tail Weight Measure
minmax Min-Max Normalization
msc Multiplicative Signal Correction
multipeak_fit Multiple Peaks Fitting

-- N --

nas Net Analyte Signal and Figures of Merit
nist_ionization_energy Ionization Energies from the NIST Atomic Spectra Database
nist_levels Energy Levels and Partition Functions from the NIST Atomic Spectra Database
nist_lines Atomic Line Data from the NIST Atomic Spectra Database
normalize Spectra Normalization

-- O --

o2pls Modified Orthogonal Projections to Latent Structures
opls Orthogonal Projections to Latent Structures
osc Orthogonal Signal Correction

-- P --

pareto_scale Pareto Scaling
partition_function Energy Levels and Partition Functions from the NIST Atomic Spectra Database
pds Piecewise Direct Standardization
peak_fit Peak Fitting
plot_boltzmann Draw a Boltzmann or Saha-Boltzmann Plot
plot_calibration Plot a Calibration Curve
plot_cell_map Cell Map of a MacroPCA or cellPCA Fit
plot_contributions Plot Q and T-squared Contributions
plot_embedding Plot a Two-Dimensional Embedding
plot_fit Plotting of Fitted Spectral Line
plot_influence Influence Plot of a PCA Model
plot_lines Overlay Emission Lines on a Spectrum
plot_loadings Loadings of a PCA as Spectra
plot_outliers Univariate Representation of Multivariate Outliers
plot_outlier_map Outlier Map of a Robust PCA
plot_som Plot a Self-Organizing Map
plot_spectra Plotting of Spectra
plot_wavelength_calibration Plot a Wavelength Calibration
poisson_scale Poisson Scaling
predict.o2pls Apply an Orthogonalization Filter to New Spectra
predict.specproc_calibration Predict from a Calibration Curve
predict.specproc_cellpca Scores and Distances of New Observations
predict.specproc_direct_orthogonal Apply an Orthogonalization Filter to New Spectra
predict.specproc_direct_osc Apply an Orthogonalization Filter to New Spectra
predict.specproc_emsc Apply EMSC to New Spectra
predict.specproc_epo Apply an Orthogonalization Filter to New Spectra
predict.specproc_filter Apply an Orthogonalization Filter to New Spectra
predict.specproc_macropca Scores and Distances of New Observations
predict.specproc_nas Net Analyte Signal of New Samples
predict.specproc_opls Predict with an OPLS Model
predict.specproc_osc Apply an Orthogonalization Filter to New Spectra
predict.specproc_projected_osc Apply an Orthogonalization Filter to New Spectra
predict.specproc_robpca Scores and Distances of New Observations
predict.specproc_som Map New Spectra onto a Self-Organizing Map
predict.specproc_wavelength_calibration Correct Wavelengths with a Wavelength Calibration
projected_osc Projected Orthogonal Signal Correction
pseudo_voigt_profile Pseudo-Voigt Function

-- Q --

quantile_weight Quantile Tail Weight Measure
q_residuals Hotelling's T-squared and Q Residuals of a PCA Model

-- R --

read_starkb Read Saved STARK-B Data
reject_shots Rejection of Outlying Laser Shots
robpca Robust Principal Component Analysis (ROBPCA)
robust_bcyj Robust Box-Cox and Yeo-Johnson Transformation
rospca Robust Sparse Principal Component Analysis (ROSPCA)
rousseeuw_croux Rousseeuw-Croux Scale Estimators

-- S --

saha_boltzmann Plasma Temperature from a Saha-Boltzmann Plot
saturation_summary Detect Saturated Channels in Spectra
savgol_derivative Derivative Order of a Savitzky-Golay Filter
savitzky_golay Savitzky-Golay Smoothing and Derivatives
self_absorption Self-Absorption Coefficient from Line Widths
snv Standard Normal Variate
som Self-Organizing Map of Spectra
som_stability Stability of a Self-Organizing Map
spectral_norm_method Norm of a Spectral Normalization
starkb_lines Stark Broadening Parameters from the STARK-B Database
stark_table Build a Table of Stark Broadening Parameters
stark_width Stark Width of a Line at Given Plasma Conditions
step_baseline Baseline Correction Recipe Step
step_cellpca cellPCA Recipe Step
step_direct_orthogonal Direct Orthogonalization Recipe Step
step_direct_osc Direct Orthogonal Signal Correction Recipe Step
step_emsc Extended Multiplicative Signal Correction Recipe Step
step_epo External Parameter Orthogonalization Recipe Step
step_glsw Generalized Least Squares Weighting Recipe Step
step_line_intensities Emission Line Intensities Recipe Step
step_line_ratio Internal Standard Normalization Recipe Step
step_macropca MacroPCA Recipe Step
step_msc Multiplicative Scatter Correction Recipe Step
step_o2pls O2PLS Filter Recipe Step for One or Several Outcomes
step_opls Orthogonal Projections to Latent Structures (OPLS) Recipe Step
step_osc Orthogonal Signal Correction Recipe Step
step_pareto_scale Pareto Scaling Recipe Step
step_poisson_scale Poisson Scaling Recipe Step
step_projected_osc Projected Orthogonal Signal Correction (OPLS Filter) Recipe Step
step_reject_shots Shot Rejection Recipe Step
step_robpca Robust PCA (ROBPCA) Recipe Step
step_robust_bcyj Robust Box-Cox and Yeo-Johnson Transformation Recipe Step
step_rospca Robust Sparse PCA (ROSPCA) Recipe Step
step_savgol Savitzky-Golay Recipe Step
step_snv Standard Normal Variate Recipe Step
step_spectral_norm Spectral Normalization Recipe Step
step_wavelet Wavelet Features Recipe Step
step_y_gradient_glsw y-Gradient Generalized Least Squares Weighting Recipe Step
summary_stats Classical or Robust Descriptive Statistics

-- T --

tukey_gh Tukey g-and-h Parametric Distribution

-- U --

umad Unbiased Median Absolute Deviation

-- V --

voigt_fwhm Full Width at Half Maximum of a Voigt Profile
voigt_profile Voigt Function

-- W --

wavelength_calibration Wavelength Calibration from Reference Lines
wavelet_features Wavelet Coefficients of Spectra
wavelet_level Number of Levels of a Wavelet Decomposition

-- Y --

y_gradient_glsw y-Gradient Generalized Least Squares Weighting

-- Z --

zscore Classical or Robust Z-Score