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 |
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 |
barbiturates | Barbiturates Spectra from .spc example files A time series of mass spectra in a list of hyperSpec objects. |
bind | Binding hyperSpec Objects |
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 |
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 |
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". |
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 |
gamma-method | Math Functions for hyperSpec Objects |
guess.wavelength | guess wavelengths from character vector |
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 |
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. |
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 |
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 |
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) |
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. |
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 |
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 |
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. |
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 |
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. |
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 |
validObject | Validation of hyperSpec objects |
validObject-method | Validation of hyperSpec objects |
vanderMonde | Function evaluation on hyperSpec objects |
vanderMonde-method | Function evaluation on hyperSpec objects |
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". |
!=-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 |