.DollarNames.hyperSpec
                        command line completion for $
Arith                   Arithmetical Operators for hyperSpec objects
Comparison              Comparison of hyperSpec objects
Math2,hyperSpec-method
                        Math Functions for hyperSpec Objects
Summary                 The functions
[,hyperSpec-method      Extract and Replace parts of hyperSpec objects
aggregate               aggregate hyperSpec objects
apply                   apply Computes summary statistics for the
                        spectra of a 'hyperSpec' object.
as.character,hyperSpec-method
                        Convert a hyperSpec object to character strings
                        for Display 'print', 'show', and 'summary' show
                        the result of 'as.character'.
as.data.frame           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
as.hyperSpec            as.hyperSpec: convenience conversion functions
barbiturates            Barbiturates Spectra from .spc example files A
                        time series of mass spectra in a list of
                        hyperSpec objects.
bind                    Binding hyperSpec Objects
chk.hy                  Validation of hyperSpec objects
chondro                 Raman spectra of 2 Chondrocytes in Cartilage A
                        Raman-map (laterally resolved Raman spectra) of
                        chondrocytes in cartilage.
colSums                 colSums, colMeans, rowSums and rowMeans
                        functions for hyperSpec objects
collapse                Collapse hyperSpec objects
cov,hyperSpec,missing-method
                        Covariance matrices for hyperSpec objects
decomposition           Convert Principal Component Decomposition or
                        the like into a hyperSpec Object
dimnames,hyperSpec-method
                        dimnames for hyperSpec objects
droplevels,hyperSpec-method
                        droplevels for hyperSpec object
empty                   Empty hyperSpec object
flu                     Quinine Fluorescence Spectra Fluorescence
                        spectra of different dilutions of quinine
                        forming a calibration set.
guess.wavelength        guess wavelengths from character vector
hy.getOptions           Options for package hyperSpec Functions to
                        access and set hyperSpec's options.
hy.unittest             hyperSpec unit tests
hyperSpec-class         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.
hyperSpec-package       Package hyperSpec
initialize              Creating a hyperSpec Object Like other S4
                        objects, a hyperSpec object can be created by
                        'new'. The hyperSpec object is then
                        'initialize'd using the given parameters.
labels<-                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                   Laser Emission A time series of an unstable
                        laser emission.
legendright             Plot multivariate data into colour channels
makeraster              makeraster
map.sel.poly            Interactively select a polygon (grid graphics)
                        and highlight points
mark.dendrogram         Mark groups in 'hclust' dendrograms
markpeak                Mark peak Marks location of the _first_
                        spectrum at the data point closes to the
                        specified position on the current plot.
matlab.palette          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.
mean_sd,numeric-method
                        Mean and Standard Deviation Calculate mean and
                        standard deviation, and mean, mean +- one
                        standard deviation, respectively.
merge,hyperSpec,hyperSpec-method
                        Merge hyperSpec objects
ncol,hyperSpec-method   The Number of Rows (Spectra), Columns, and Data
                        Points per Spectrum of an hyperSpec Object)
normalize01             normalization for mixed colors
orderwl                 Sorting the Wavelengths of a hyperSpec Object
                        Rearranges the 'hyperSpec' object so that the
                        wavelength vector is in increasing (or
                        decreasing) order.
paracetamol             Paracetamol Spectrum A Raman spectrum of a
                        paracetamol tablet.
pearson.dist            Distance based on Pearson's R squared
plot-methods            Plotting hyperSpec Objects
plotc                   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.
plotmap                 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.
plotmat                 Plot spectra matrix
plotspc                 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.
qplotc                  Spectra plotting with ggplot2
qplotmap                Spectra plotting with ggplot2
qplotmixmap             qplotmap with colour mixing for multivariate
                        overlay
qplotspc                Spectra plotting with ggplot2
rbind.fill.matrix       Bind matrices by row, and fill missing columns
                        with NA
read.ENVI.Nicolet       Import of ENVI data as hyperSpec object
read.cytomat            Import for Cytospec mat files
read.ini                Read INI files
read.jdx                JCAMP-DX Import for Shimadzu Library Spectra
read.spc                Import for Thermo Galactic's spc file format
                        These functions allow to import Thermo
                        Galactic/Grams .spc files.
read.spc.Kaiser         read Kaiser .spc files
read.spe                Import WinSpec SPE file
read.txt.Horiba         Import Horiba Labspec exported ASCII files
read.txt.Shimadzu       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)
read.txt.long           Import and Export of hyperSpec objects Besides
                        'save' and 'load', two general ways to import
                        and export data into 'hyperSpec' objects exist.
rmmvnorm                Multivariate normal random numbers
sample,hyperSpec-method
                        Random Samples and Permutations Take a sample
                        of the specified size from the elements of x
                        with or without replacement.
scale,hyperSpec-method
                        Center and scale hyperSpec object
seq.hyperSpec           Sequence generation along spectra or
                        wavelengths This function generates sequences
                        along the spectra (rows) or wavelengths of
                        hyperSpec objects.
spc.NA.approx           Impute missing data points
spc.bin                 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.
spc.fit.poly            Polynomial Baseline Fitting These functions fit
                        polynomal baselines.
spc.identify            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'.
spc.loess               loess smoothing interpolation for spectra
                        Spectra can be smoothed and interpolated on a
                        new wavelength axis using 'loess'.
spc.rubberband          Rubberband baseline correction
spc.smooth.spline       Spectral smoothing by splines
split                   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                  subset
sweep                   Sweep Summary Statistic out of an hyperSpec
                        Object 'sweep' for 'hyperSpec' objects.
trellis.factor.key      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.
vanderMonde             Function evaluation on hyperSpec objects
wc                      wc word count of ASCII files
wl                      Getting and Setting the Wavelength Axis 'wl'
                        returns the wavelength axis, 'wl<-' sets it.
wl.eval                 Evaluate function on wavelengths of hyperSpec
                        object
wl2i                    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.
wlconv                  Convert different wavelength units
