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

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Documentation for package ‘hyperSpec’ version 0.100.2

• 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