Package index • libscanR

Package

libscanR libscanR-package: libscanR: Analysis and Visualization of LIBS Spectra

Import & Export

ls_read_spectrum(): Read a LIBS Spectrum from File
ls_read_dir(): Read All Spectra from a Directory
ls_read_csv(): Read a LIBS Spectrum from CSV (Convenience Wrapper)
ls_read_sciaps(): Read SciAps LIBS Data
ls_read_aurora(): Read Applied Spectra / Aurora Data
ls_read_auto(): Auto-Detect and Read LIBS Data
ls_write_csv(): Write a LIBS Spectrum to CSV
ls_export_spectra(): Export a LIBS Dataset to a Directory

Data Structures

ls_spectrum(): Create a LIBS Spectrum Object
ls_dataset(): Create a LIBS Dataset
ls_calibration(): Create a LIBS Calibration Model
is_libs_spectrum(): Test whether an object is a libs_spectrum
is_libs_dataset(): Test whether an object is a libs_dataset
is_libs_calibration(): Test whether an object is a libs_calibration

Preprocessing

ls_baseline(): Baseline Correction
ls_normalize(): Normalize Spectra
ls_smooth(): Smooth Spectra
ls_crop(): Crop Spectral Range
ls_average_shots(): Average Replicate Shots
ls_gate_optimize(): Gate Delay Optimization

Peak Analysis

ls_find_peaks(): Find Emission Peaks
ls_identify_peaks(): Identify Peaks Against the NIST Line Database
ls_peak_area(): Calculate Peak Area
ls_element_db(): NIST Emission Line Database

Calibration & Quantification

ls_calibrate(): Build Calibration Curve
ls_saha_boltzmann(): Calibration-Free LIBS via Saha-Boltzmann
ls_quantify(): Quantify Element Concentration
ls_lod(): Limit of Detection (3-sigma)
ls_loq(): Limit of Quantification (10-sigma)

Chemometrics

ls_pca(): Principal Component Analysis of LIBS Spectra
ls_plsda(): PLS-DA Classification
ls_cluster(): Cluster LIBS Spectra
ls_classify(): Classify Unknown Spectra
ls_train_classifier(): Train a Classifier

Spatial Mapping

ls_build_map(): Build a Spatial Elemental Map
ls_map_elements(): Build Maps for Multiple Elements

Tissue Analysis

ls_tissue_classify(): Tissue Classification via LIBS
ls_tissue_discriminate(): Tissue Discrimination Analysis

Visualization

ls_plot_spectrum(): Plot a LIBS Spectrum
ls_plot_overlay(): Overlay Multiple Spectra
ls_plot_region(): Plot a Spectral Region in Detail
ls_plot_calibration(): Plot a Calibration Curve
ls_plot_residuals(): Plot Calibration Residuals
ls_plot_map(): Plot an Elemental Map
ls_plot_map_panel(): Plot Multi-Element Map Panel
ls_plot_element_map(): Plot an Element Map (alias)
ls_plot_pca(): Plot PCA Scores
ls_plot_loadings(): Plot PCA Loadings
ls_plot_scree(): Plot PCA Variance (Scree Plot)
ls_plot_plsda(): Plot PLS-DA Results
theme_libs(): LIBS Theme for ggplot2
scale_color_wavelength(): Wavelength-Based Color Scale

Shiny Application

ls_run_app(): Launch the libscanR Shiny Application

Example Data

ls_simulate_spectrum(): Simulate a LIBS Spectrum
ls_example_data(): Generate Example LIBS Dataset

S3 Methods

c(<libs_spectrum>): Combine Multiple LIBS Spectra by Stacking Shots
dim(<libs_dataset>): Dimensions of a Dataset (spectra x channels)
dim(<libs_spectrum>): Dimensions of a LIBS Spectrum (shots x channels)
length(<libs_dataset>): Number of Spectra in a Dataset
length(<libs_spectrum>): Number of Channels in a LIBS Spectrum
plot(<libs_dataset>): Plot a LIBS Dataset
plot(<libs_spectrum>): Plot a LIBS Spectrum
predict(<libs_calibration>): Predict Concentrations from a Calibration Model
print(<libs_calibration>): Print a LIBS Calibration
print(<libs_dataset>): Print a LIBS Dataset
print(<libs_spectrum>): Print a LIBS Spectrum
`[`(<libs_dataset>): Subset a LIBS Dataset
`[`(<libs_spectrum>): Subset a LIBS Spectrum by Wavelength
summary(<libs_calibration>): Summary of a LIBS Calibration
summary(<libs_dataset>): Summary of a LIBS Dataset
summary(<libs_spectrum>): Summary of a LIBS Spectrum