hyperSpec

Arithmetical Operators for hyperSpec objects

Comparison of hyperSpec objects

Future functions

aggregate hyperSpec objects

apply Computes summary statistics for the spectra of a hyperSpec object.

as.hyperSpec: convenience conversion functions

Conversion of a hyperSpec object into a data.frame or matrix as.data.frame returns x@data (as data.frame) as.matrix returns the spectra matrix x@data$spc as matrix

Barbiturates Spectra from .spc example files A time series of mass spectra in a list of hyperSpec objects.

Polynomial Baseline Fitting These functions fit polynomal baselines.

Binding hyperSpec Objects

Validation of hyperSpec objects

Raman spectra of 2 Chondrocytes in Cartilage A Raman-map (laterally resolved Raman spectra) of chondrocytes in cartilage.

colSums, colMeans, rowSums and rowMeans functions for hyperSpec objects

Collapse hyperSpec objects

count lines (of an ASCII file)

Covariance matrices for hyperSpec objects

Convert Principal Component Decomposition or the like into a hyperSpec Object

The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an hyperSpec Object)

dimnames for hyperSpec objects

command line completion for $

Find clusters of approximately equal wavelengths

Try finding groups of hyperSpec objects with (approximately) equal wavelength axes

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

droplevels for hyperSpec object

Empty hyperSpec object

Extract and Replace parts of hyperSpec objects

Quinine Fluorescence Spectra Fluorescence spectra of different dilutions of quinine forming a calibration set.

guess wavelengths from character vector

Class "hyperSpec" This class handles hyperspectral data sets, i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with the spectra.

Package hyperSpec

Creating a hyperSpec Object

Get and Set Labels of a hyperSpec Object value may be a list or vector of labels giving the new label for each of the entries specified by which.

Laser Emission A time series of an unstable laser emission.

Plot a Map and Identify/Select Spectra in the Map levelplot functions for hyperSpec objects. An image or map of a summary value of each spectrum is plotted. Spectra may be identified by mouse click.

makeraster

Interactively select a polygon (grid graphics) and highlight points

Mark groups in hclust dendrograms

Mark peak Marks location of the first spectrum at the data point closest to the specified position on the current plot.

Math Functions for hyperSpec Objects

Mean and Standard Deviation Calculate mean and standard deviation, and mean, mean +- one standard deviation, respectively.

Merge hyperSpec objects

normalization for mixed colors

Options for package hyperSpec Functions to access and set hyperSpec's options.

Sorting the Wavelengths of a hyperSpec Object Rearranges the hyperSpec object so that the wavelength vector is in increasing (or decreasing) order.

Matlab-like Palettes Two palettes going from blue over green to red, approximately as the standard palette of Matlab does. The second one has darker green values and is better suited for plotting lines on white background.

Paracetamol Spectrum A Raman spectrum of a paracetamol tablet.

Distance based on Pearson's R squared

Plotting hyperSpec Objects

Calibration- and Timeseries Plots, Depth-Profiles and the like plotc plots intensities of a hyperSpec object over another dimension such as concentration, time, or a spatial coordinate.

Plot spectra matrix

Plotting Spectra Plot the spectra of a hyperSpec object, i.e. intensity over wavelength. Instead of the intensity values of the spectra matrix summary values calculated from these may be used.

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 converts a list to a data frame, but doesn't do any checks to make sure it's a valid format. Much faster.

Bind matrices by row, and fill missing columns with NA

Read INI files

Import for Thermo Galactic's spc file format These functions allow to import Thermo Galactic/Grams .spc files.

read Kaiser .spc files

Import of ENVI data as hyperSpec object

File Import Andor Solis

File import filter PerkinElmer ASCII spectra

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

Reads Shimadzu GCxGC-qMS - Spectra Files (.txt) as exported by Shimadzu Chrome Solution (v. 2.72) Mass Spectrometer: Shimadzu GCMS-QP 2010 Ultra (www.shimadzu.com)

File Import Witec Raman

Multivariate normal random numbers

Random Samples and Permutations Take a sample of the specified size from the elements of x with or without replacement.

Center and scale hyperSpec object

Sequence generation along spectra or wavelengths This function generates sequences along the spectra (rows) or wavelengths of hyperSpec objects.

Convert a hyperSpec object to character strings for Display print, show, and summary show the result of as.character.

Wavelength Binning In order to reduce the spectral resolution and thus gain signal to noise ratio or to reduce the dimensionality of the spectral data set, the spectral resolution can be reduced.

Identifying Spectra and Spectral Data Points This function allows to identify the spectrum and the wavelength of a point in a plot produced by plotspc.

loess smoothing interpolation for spectra Spectra can be smoothed and interpolated on a new wavelength axis using loess.

Rubberband baseline correction

Spectral smoothing by splines

Impute missing data points

Split a hyperSpec object according to groups split divides the hyperSpec object into a list of hyperSpec objects according to the groups given by f.

subset

The functions

Sweep Summary Statistic out of an hyperSpec Object sweep for hyperSpec objects.

Import/export of hyperSpec objects to/from ASCII files A detailed discussion of hyperSpec's file import and export capabilities is given in vignette “fileio”.

Color coding legend for factors Modifies a list of lattice arguments (as for levelplot, etc.) according to the factor levels. The colorkey will shows all levels (including unused), and the drawing colors will be set accordingly.

hyperSpec unit tests

Function evaluation on hyperSpec objects

line/word/character count of ASCII files

Getting and Setting the Wavelength Axis wl returns the wavelength axis, wl<- sets it.

Evaluate function on wavelengths of hyperSpec object

Conversion between Wavelength and Spectra Matrix Column Index wl2i returns the column indices for the spectra matrix for the given wavelengths. i2wl converts column indices into wavelengths.

Convert different wavelength units