# Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

## Documentation for package ‘hyperSpec’ version 0.100.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N O P Q R S T V W misc

hyperSpec-package | Package hyperSpec

## -- A --

abs-method | Math Functions for hyperSpec Objects
acos-method | Math Functions for hyperSpec Objects
acosh-method | Math Functions for hyperSpec Objects
aggregate | aggregate hyperSpec objects
aggregate-method | aggregate hyperSpec objects
all-method | The functions
all.equal | Comparison of hyperSpec objects
all.equal-method | Comparison of hyperSpec objects
all_wl | The functions
alois.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.
any-method | The functions
any_wl | The functions
apply | apply Computes summary statistics for the spectra of a 'hyperSpec' object.
apply-method | apply Computes summary statistics for the spectra of a 'hyperSpec' object.
Arith | Arithmetical Operators for hyperSpec objects
Arith-method | Arithmetical Operators for hyperSpec objects
as.character | Convert a hyperSpec object to character strings for Display 'print', 'show', and 'summary' show the result of 'as.character'.
as.character-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$spc' as matrix
as.data.frame-method | Conversion of a hyperSpec object into a data.frame or matrix 'as.data.frame' returns 'x@data' (as data.frame) 'as.matrix' returns the spectra matrix 'x@data$spc' as matrix
as.data.frame.hyperSpec | 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$spc' as matrix
as.hyperSpec | as.hyperSpec: convenience conversion functions
as.hyperSpec-method | as.hyperSpec: convenience conversion functions
as.long.df | Conversion of a hyperSpec object into a data.frame or matrix 'as.data.frame' returns 'x@data' (as data.frame) 'as.matrix' returns the spectra matrix 'x@data$spc' as matrix
as.matrix | 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$spc' as matrix
as.matrix-method | Conversion of a hyperSpec object into a data.frame or matrix 'as.data.frame' returns 'x@data' (as data.frame) 'as.matrix' returns the spectra matrix 'x@data$spc' as matrix
as.matrix.hyperSpec | 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$spc' as matrix
as.t.df | Conversion of a hyperSpec object into a data.frame or matrix 'as.data.frame' returns 'x@data' (as data.frame) 'as.matrix' returns the spectra matrix 'x@data$spc' as matrix
as.wide.df | 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
asin-method | Math Functions for hyperSpec Objects
asinh-method | Math Functions for hyperSpec Objects
assert_hyperSpec | Future functions
atan-method | Math Functions for hyperSpec Objects
atanh-method | Math Functions for hyperSpec Objects
ave-method | aggregate hyperSpec objects

## -- B --

barbiturates | Barbiturates Spectra from .spc example files A time series of mass spectra in a list of hyperSpec objects.
bind | Binding hyperSpec Objects

## -- C --

cbind.hyperSpec | Binding hyperSpec Objects
cbind2-method | Binding hyperSpec Objects
ceiling-method | Math Functions for 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.
collapse | Collapse hyperSpec objects
collapse.hyperSpec | Collapse hyperSpec objects
colMeans-method | colSums, colMeans, rowSums and rowMeans functions for hyperSpec objects
colmix.rgb | Plot multivariate data into colour channels
colnames | dimnames for hyperSpec objects
colnames-method | dimnames for hyperSpec objects
colnames<- | dimnames for hyperSpec objects
colnames<--method | dimnames for hyperSpec objects
colSums | colSums, colMeans, rowSums and rowMeans functions for hyperSpec objects
colSums-method | colSums, colMeans, rowSums and rowMeans functions for hyperSpec objects
Compare-method | Comparison of hyperSpec objects
Comparison | Comparison of hyperSpec objects
cos-method | Math Functions for hyperSpec Objects
cosh-method | Math Functions for hyperSpec Objects
count_lines | count lines (of an ASCII file)
cov-method | Covariance matrices for hyperSpec objects
create | Creating a hyperSpec Object
create-method | Creating a hyperSpec Object
cummax-method | Math Functions for hyperSpec Objects
cummin-method | Math Functions for hyperSpec Objects
cumprod-method | Math Functions for hyperSpec Objects
cumsum-method | Math Functions for hyperSpec Objects

## -- D --

decomposition | Convert Principal Component Decomposition or the like into a hyperSpec Object
digamma-method | Math Functions for hyperSpec Objects
dim-method | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an hyperSpec Object)
dimnames | dimnames for hyperSpec objects
dimnames-method | dimnames for hyperSpec objects
droplevels-method | droplevels for hyperSpec object

## -- E --

empty | Empty hyperSpec object
ev2freq | Convert different wavelength units
ev2invcm | Convert different wavelength units
ev2nm | Convert different wavelength units
ev2raman | Convert different wavelength units
exp-method | Math Functions for hyperSpec Objects
expm1-method | Math Functions for hyperSpec Objects
export | 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".

## -- F --

fitraster | makeraster
floor-method | Math Functions for hyperSpec Objects
flu | Quinine Fluorescence Spectra Fluorescence spectra of different dilutions of quinine forming a calibration set.
freq2ev | Convert different wavelength units
freq2invcm | Convert different wavelength units
freq2nm | Convert different wavelength units
freq2raman | Convert different wavelength units
Future-functions | Future functions

## -- G --

gamma-method | Math Functions for hyperSpec Objects
guess.wavelength | guess wavelengths from character vector

## -- H --

hy.getOption | Options for package hyperSpec Functions to access and set hyperSpec's options.
hy.getOptions | Options for package hyperSpec Functions to access and set hyperSpec's options.
hy.setOptions | 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.
hy_get_option | Future functions
hy_set_options | Future functions

## -- I --

i2wl | 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.
import | 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".
initialize | Creating a hyperSpec Object
initialize-method | Creating a hyperSpec Object
invcm2ev | Convert different wavelength units
invcm2freq | Convert different wavelength units
invcm2nm | Convert different wavelength units
invcm2raman | Convert different wavelength units
is.na-method | The functions
isample | Random Samples and Permutations Take a sample of the specified size from the elements of x with or without replacement.

## -- L --

labels-method | 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'.
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'.
labels<--method | 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
length-method | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an hyperSpec Object)
levelplot-method | 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.
lgamma-method | Math Functions for hyperSpec Objects
log | Math Functions for hyperSpec Objects
log-method | Math Functions for hyperSpec Objects
log1p-method | Math Functions for hyperSpec Objects

## -- M --

makeraster | makeraster
map.identify | 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.
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 closest to the specified position on the current plot.
Math | Math Functions for hyperSpec Objects
Math-method | Math Functions for hyperSpec Objects
Math2 | Math Functions for hyperSpec Objects
Math2-method | Math Functions for hyperSpec Objects
matlab.dark.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.
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.
max-method | The functions
mean-method | Mean and Standard Deviation Calculate mean and standard deviation, and mean, mean +- one standard deviation, respectively.
mean_pm_sd | Mean and Standard Deviation Calculate mean and standard deviation, and mean, mean +- one standard deviation, respectively.
mean_pm_sd-method | Mean and Standard Deviation Calculate mean and standard deviation, and mean, mean +- one standard deviation, respectively.
mean_sd | Mean and Standard Deviation Calculate mean and standard deviation, and mean, mean +- one standard deviation, respectively.
mean_sd-method | Mean and Standard Deviation Calculate mean and standard deviation, and mean, mean +- one standard deviation, respectively.
merge | Merge hyperSpec objects
merge-method | Merge hyperSpec objects
min-method | The functions

## -- N --

ncol-method | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an hyperSpec Object)
new | Creating a hyperSpec Object
new-method | Creating a hyperSpec Object
nm2ev | Convert different wavelength units
nm2freq | Convert different wavelength units
nm2invcm | Convert different wavelength units
nm2raman | Convert different wavelength units
normalize.colrange | Plot multivariate data into colour channels
normalize.minmax | Plot multivariate data into colour channels
normalize.null | Plot multivariate data into colour channels
normalize.range | Plot multivariate data into colour channels
normalize01 | normalization for mixed colors
normalize01-method | normalization for mixed colors
nrow-method | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an hyperSpec Object)
nwl | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an hyperSpec Object)

## -- O --

Operators | Comparison of hyperSpec objects
orderwl | Sorting the Wavelengths of a hyperSpec Object Rearranges the 'hyperSpec' object so that the wavelength vector is in increasing (or decreasing) order.

## -- P --

paracetamol | Paracetamol Spectrum A Raman spectrum of a paracetamol tablet.
pearson.dist | Distance based on Pearson's R squared
plot | Plotting hyperSpec Objects
plot-method | Plotting hyperSpec Objects
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.
plotvoronoi | 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.
pooled.cov | Covariance matrices for hyperSpec objects
print | Convert a hyperSpec object to character strings for Display 'print', 'show', and 'summary' show the result of 'as.character'.
print-method | Convert a hyperSpec object to character strings for Display 'print', 'show', and 'summary' show the result of 'as.character'.
prod-method | The functions

## -- Q --

qmixlegend | Plot multivariate data into colour channels
qmixtile | Plot multivariate data into colour channels
qplotc | Spectra plotting with ggplot2
qplotmap | Spectra plotting with ggplot2
qplotmixmap | qplotmap with colour mixing for multivariate overlay
qplotspc | Spectra plotting with ggplot2
quantile-method | Mean and Standard Deviation Calculate mean and standard deviation, and mean, mean +- one standard deviation, respectively.

## -- R --

raman2ev | Convert different wavelength units
raman2freq | Convert different wavelength units
raman2invcm | Convert different wavelength units
raman2nm | Convert different wavelength units
range-method | The functions
rbind.fill | Bind matrices by row, and fill missing columns with NA
rbind.fill.matrix | Bind matrices by row, and fill missing columns with NA
rbind.hyperSpec | Binding hyperSpec Objects
rbind2-method | Binding hyperSpec Objects
read.asc.PerkinElmer | File import filter PerkinElmer ASCII spectra
read.cytomat | Import for Cytospec mat files
read.ENVI | Import of ENVI data as hyperSpec object
read.ENVI.HySpex | Import of ENVI data as hyperSpec object
read.ENVI.Nicolet | Import of ENVI data as hyperSpec object
read.ini | Read INI files
read.jdx | JCAMP-DX Import for Shimadzu Library Spectra
read.mat.Cytospec | Import for Cytospec mat files
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.spc.KaiserLowHigh | read Kaiser .spc files
read.spc.KaiserMap | read Kaiser .spc files
read.spe | Import WinSpec SPE file
read.txt.Horiba | Import Horiba Labspec exported ASCII files
read.txt.Horiba.t | Import Horiba Labspec exported ASCII files
read.txt.Horiba.xy | Import Horiba Labspec exported ASCII files
read.txt.long | 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".
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.wide | 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".
read_txt_long | Future functions
read_txt_wide | Future functions
rmmvnorm | Multivariate normal random numbers
rmmvnorm-method | Multivariate normal random numbers
round-method | Math Functions for hyperSpec Objects
rowMeans-method | colSums, colMeans, rowSums and rowMeans functions for hyperSpec objects
rownames | dimnames for hyperSpec objects
rownames-method | dimnames for hyperSpec objects
rownames<- | dimnames for hyperSpec objects
rownames<--method | dimnames for hyperSpec objects
rowSums-method | colSums, colMeans, rowSums and rowMeans functions for hyperSpec objects

## -- S --

sample-method | Random Samples and Permutations Take a sample of the specified size from the elements of x with or without replacement.
scale | Center and scale hyperSpec object
scale-method | Center and scale hyperSpec object
scale-methods | Center and scale hyperSpec object
sel.poly | Interactively select a polygon (grid graphics) and highlight points
seq | Sequence generation along spectra or wavelengths This function generates sequences along the spectra (rows) or wavelengths of hyperSpec objects.
seq-method | Sequence generation along spectra or wavelengths This function generates sequences along the spectra (rows) or wavelengths of hyperSpec objects.
seq.hyperSpec | Sequence generation along spectra or wavelengths This function generates sequences along the spectra (rows) or wavelengths of hyperSpec objects.
show | Convert a hyperSpec object to character strings for Display 'print', 'show', and 'summary' show the result of 'as.character'.
show-method | Convert a hyperSpec object to character strings for Display 'print', 'show', and 'summary' show the result of 'as.character'.
sign-method | Math Functions for hyperSpec Objects
signif-method | Math Functions for hyperSpec Objects
sin-method | Math Functions for hyperSpec Objects
sinh-method | Math Functions for hyperSpec Objects
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.fit.poly.below | 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.label.default | 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.label.wlonly | 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.NA.approx | Impute missing data points
spc.NA.linapprox | Impute missing data points
spc.point.default | 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.point.max | 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.point.min | 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.point.sqr | 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.rubberband | Rubberband baseline correction
spc.smooth.spline | Spectral smoothing by splines
spe.showcalpoints | Import WinSpec SPE file
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'.
split-method | 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'.
split-methods | 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'.
sqrt-method | Math Functions for hyperSpec Objects
stacked.offsets | 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.
subset | subset
subset-method | subset
sum-method | The functions
Summary | The functions
summary | Convert a hyperSpec object to character strings for Display 'print', 'show', and 'summary' show the result of 'as.character'.
Summary-method | The functions
summary-method | Convert a hyperSpec object to character strings for Display 'print', 'show', and 'summary' show the result of 'as.character'.
sweep | Sweep Summary Statistic out of an hyperSpec Object 'sweep' for 'hyperSpec' objects.
sweep-method | Sweep Summary Statistic out of an hyperSpec Object 'sweep' for 'hyperSpec' objects.
sweep-methods | Sweep Summary Statistic out of an hyperSpec Object 'sweep' for 'hyperSpec' objects.

## -- T --

tan-method | Math Functions for hyperSpec Objects
tanh-method | Math Functions 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.
trigamma-method | Math Functions for hyperSpec Objects
trunc-method | Math Functions for hyperSpec Objects

## -- V --

validObject | Validation of hyperSpec objects
validObject-method | Validation of hyperSpec objects
vanderMonde | Function evaluation on hyperSpec objects
vanderMonde-method | Function evaluation on hyperSpec objects

## -- W --

wc | line/word/character 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.
wl<- | Getting and Setting the Wavelength Axis 'wl' returns the wavelength axis, 'wl<-' sets it.
wlconv | Convert different wavelength units
wl_convert_units | Future functions
write.txt.long | 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".
write.txt.wide | 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".

## -- misc --

!=-method | Comparison of hyperSpec objects
$ | Extract and Replace parts of hyperSpec objects
$-method | Extract and Replace parts of hyperSpec objects
$<- | Extract and Replace parts of hyperSpec objects
$<--method | Extract and Replace parts of hyperSpec objects
%%-method | Arithmetical Operators for hyperSpec objects
%*% | Arithmetical Operators for hyperSpec objects
%*%-method | Arithmetical Operators for hyperSpec objects
%/%-method | Arithmetical Operators for hyperSpec objects
*-method | Arithmetical Operators for hyperSpec objects
+-method | Arithmetical Operators for hyperSpec objects
--method | Arithmetical Operators for hyperSpec objects
.cluster.wavelengths | Find clusters of approximately equal wavelengths
.collapse.equal | Try finding groups of hyperSpec objects with (approximately) equal wavelength axes
.DollarNames | command line completion for $
.DollarNames-method | command line completion for $
.DollarNames.hyperSpec | command line completion for $
.fix_spc_colnames | Ensure that the spectra matrix has the wavelengths in column names
.read.spe.header | Import WinSpec SPE file
.read.spe.xml | Read XML footer from SPE file format version 3.0
.read.spe.xml_string | .read.spe.xml_string
.spc_io_postprocess_optional | Future functions
.wl_fix_unit_name | Future functions
/-method | Arithmetical Operators for hyperSpec objects
<-method | Comparison of hyperSpec objects
<=-method | Comparison of hyperSpec objects
==-method | Comparison of hyperSpec objects
>-method | Comparison of hyperSpec objects
>=-method | Comparison of hyperSpec objects
[ | Extract and Replace parts of hyperSpec objects
[-method | Extract and Replace parts of hyperSpec objects
[<- | Extract and Replace parts of hyperSpec objects
[<--method | Extract and Replace parts of hyperSpec objects
[[ | Extract and Replace parts of hyperSpec objects
[[-method | Extract and Replace parts of hyperSpec objects
[[<- | Extract and Replace parts of hyperSpec objects
[[<--method | Extract and Replace parts of hyperSpec objects
^-method | Arithmetical Operators for hyperSpec objects