Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)
Future functions
guess wavelengths from character vector
normalization for mixed colors
Reads Shimadzu GCxGC-qMS - Spectra Files (.txt) as exported by Shimadz...
Extract and Replace parts of hyperSpec objects
Convert Principal Component Decomposition or the like into a hyperSpec...
droplevels for hyperSpec object
hyperSpec unit tests
aggregate hyperSpec objects
apply Computes summary statistics for the spectra of a hyperSpec obj...
Empty hyperSpec object
Arithmetical Operators for hyperSpec objects
as.hyperSpec: convenience conversion functions
Conversion of a hyperSpec object into a data.frame or matrix `as.data....
Polynomial Baseline Fitting These functions fit polynomal baselines.
Comparison of hyperSpec objects
Binding hyperSpec Objects
Validation of hyperSpec objects
Raman spectra of 2 Chondrocytes in Cartilage A Raman-map (laterally re...
Collapse hyperSpec objects
colSums, colMeans, rowSums and rowMeans functions for hyperSpec object...
count lines (of an ASCII file)
Covariance matrices for hyperSpec objects
The Number of Rows (Spectra), Columns, and Data Points per Spectrum of...
dimnames for hyperSpec objects
command line completion for $
Find clusters of approximately equal wavelengths
Try finding groups of hyperSpec objects with (approximately) equal wav...
Helper function to harmonize treatment of file import results
Ensure that the spectra matrix has the wavelengths in column names
Read XML footer from SPE file format version 3.0
.read.spe.xml_string
Class "hyperSpec" This class handles hyperspectral data sets, i.e. spa...
Package hyperSpec
Creating a hyperSpec Object
Get and Set Labels of a hyperSpec Object value may be a list or vect...
Plot a Map and Identify/Select Spectra in the Map levelplot function...
makeraster
Interactively select a polygon (grid graphics) and highlight points
Mark groups in hclust dendrograms
Mark peakMarks location of the first spectrum at the data point cl...
Math Functions for hyperSpec Objects
Mean and Standard Deviation Calculate mean and standard deviation, and...
Merge hyperSpec objects
Options for package hyperSpec Functions to access and set hyperSpec's ...
Sorting the Wavelengths of a hyperSpec Object Rearranges the `hyperSpe...
Matlab-like Palettes Two palettes going from blue over green to red, a...
Distance based on Pearson's
Plotting hyperSpec Objects
Calibration- and Timeseries Plots, Depth-Profiles and the like plotc...
Plot spectra matrix
Plotting Spectra Plot the spectra of a hyperSpec object, i.e. intens...
Spectra plotting with ggplot2
Spectra plotting with ggplot2
Plot multivariate data into colour channels
qplotmap with colour mixing for multivariate overlay
Spectra plotting with ggplot2
Quick data frame. Experimental version of as.data.frame that convert...
Bind matrices by row, and fill missing columns with NA
Read INI files
read Kaiser .spc files
Import for Thermo Galactic's spc file format These functions allow to ...
File Import Andor Solis
File import filter PerkinElmer ASCII spectra
Import of ENVI data as hyperSpec object
JCAMP-DX Import for Shimadzu Library Spectra
Import for Cytospec mat files
Import WinSpec SPE file
Import Horiba Labspec exported ASCII files
import Raman measurements from Renishaw ASCII-files
File Import Witec Raman
Multivariate normal random numbers
Random Samples and Permutations Take a sample of the specified size fr...
Center and scale hyperSpec object
Sequence generation along spectra or wavelengths This function generat...
Convert a hyperSpec object to character strings for Display print, `...
Wavelength Binning In order to reduce the spectral resolution and thus...
Identifying Spectra and Spectral Data Points This function allows to i...
loess smoothing interpolation for spectra Spectra can be smoothed and ...
Rubberband baseline correction
Spectral smoothing by splines
Impute missing data points
Split a hyperSpec object according to groups split divides the `hype...
subset
The functions
Sweep Summary Statistic out of an hyperSpec Object sweep for `hyperS...
Import/export of hyperSpec objects to/from ASCII files A detailed disc...
Color coding legend for factors Modifies a list of lattice arguments (...
Function evaluation on hyperSpec objects
line/word/character count of ASCII files
Evaluate function on wavelengths of hyperSpec object
Getting and Setting the Wavelength Axis wl returns the wavelength ax...
Conversion between Wavelength and Spectra Matrix Column Index wl2i r...
Convert different wavelength units
Comfortable ways to work with hyperspectral data sets. I.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.
Useful links