.DollarNames.hyperSpec
                        command line completion for $
Math2                   Math Functions for hyperSpec Objects
Summary                 The functions
[                       Extract and Replace parts of hyperSpec objects
aggregate               aggregate hyperSpec objects
all.equal               Comparison of hyperSpec objects
apply                   apply Computes summary statistics for the
                        spectra of a 'hyperSpec' object.
as.character            Convert a hyerSpec 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
barbiturates            Barbiturates Spectra from .spc example files A
                        time series of mass spectra in a list of
                        hyperSpec objects.
bind                    Binding hyperSpec Objects Two S3 functions
                        'cbind.hyperSpec' and 'rbind.hyperSpec' act as
                        an interfaces to 'cbind2' and 'rbind2' because
                        neither 'rBind' and 'cBind' nor S4 versions of
                        'cbind' and 'rbind' do work at the moment.
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                 functions for hyperSpec objects
collapse                Collapse hyperSpec objects
decomposition           Convert Principal Component Decomposition or
                        the like into a hyperSpec Object Decomposition
                        of the spectra matrix is a common procedure in
                        chemometrix data analysis. 'decomposition'
                        converts the result matrices into new
                        'hyperSpec' objects.
dimnames                Dimnames for hyperSpec objects
empty                   Empty hyperSpec object
flu                     Quinine Fluorescence Spectra Fluorescence
                        spectra of different dilutions of quinine
                        forming a calibration set.
hy.getOptions           Options for package hyperSpec Functions to
                        access and set hyperSpec's options.
hy.unittest             hyperSpec unit tests If 'svUnit' is available,
                        run the unit tests and display the results.
hyperSpec Arith         Arithmetical Operators: +, -, *, /, ^, %%, %/%,
                        %*%
hyperSpec-class         Class "hyperSpec"
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
logbook                 Logging the processing ot a hyperSpec Object
                        Extracts the slot '@log' of a 'hyperSpec'
                        object.
logentry                Append a Row to the logbook of a hyperSpec
                        Object A log entry is generated and appended to
                        the log of 'x'.
map.sel.poly            Interactively select a polygon (grid graphics)
                        and highlight points
mark.dendrogram         Mark groups in 'hclust' dendrograms
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                 Mean and Standard Deviation Calculate mean and
                        standard deviation, and mean, mean +- one
                        standard deviation, respectively.
merge                   Merge hyperSpec objects
ncol                    The Number of Rows (Spectra), Columns, and Data
                        Points per Spectrum of an hyperSpec Object)
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.
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       Nicolet uses some more keywords in their header
                        file. 'read.ENVI.Nicolet' therefore appends
                        "description", "z plot titles", and "pixel
                        size" to 'keys.hdr2log' before calling
                        'read.ENVI'. They are then interpreted as
                        follows: description giving the position of the
                        first spectrum z plot titles wavelength and
                        intensity axis units, comma separated pixel
                        size interpreted as x and y step size
read.jdx.Shimadzu       JCAMP-DX Import for Shimadzu Library Spectra
read.spc.KaiserMap      'read.spc.KaiserMap' imports sets of .spc files
                        of Raman maps written by Kaiser Optical
                        Systems' Hologram software.  It may also serve
                        as an example how to write wrapper functions
                        for 'read.spc' to conveniently import
                        specialized sets of .spc files.
read.txt.Shimadzu       Reads Shimadzu Spectra Files (.txt) as exported
                        by Shimadzu Chrome Solution (v. 2.73)
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.
sample                  Random Samples and Permutations Take a sample
                        of the specified size from the elements of x
                        with or without replacement.
scan.txt.Renishaw       import Raman measurements from Renishaw
                        ASCII-files import Raman measurements from
                        Renishaw (possibly compressed) .txt file.
scan.txt.Witec          File Import Witec Raman
sel.poly                Interactively select a polygon (grid graphics)
seq.hyperSpec           Sequence generation along spectra or
                        wavelengths This function generates sequences
                        along the spectra (rows) or wavelengths of
                        hyperSpec objects.
spc.NA.linapprox        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'.
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.
wc                      wc word count of ASCII files
wl                      Getting and Setting the Wavelength Axis 'wl'
                        returns the wavelength axis, 'wl<-' sets it.
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.
