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 |
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 |
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 |
atan-method |
Math Functions for hyperSpec Objects |
atanh-method |
Math Functions for hyperSpec Objects |
ave-method |
aggregate 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 |
cov-method |
Covariance matrices for hyperSpec objects |
create |
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. |
create-method |
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. |
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 |
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 and Export of hyperSpec objects Besides 'save' and 'load', two general ways to import and export data into 'hyperSpec' objects exist. |
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. |
initialize-method |
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. |
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 closes 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 Like other S4 objects, a hyperSpec object can be created by 'new'. The hyperSpec object is then 'initialize'd using the given parameters. |
new-method |
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. |
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) |
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 |
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. |
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. |
wl<- |
Getting and Setting the Wavelength Axis 'wl' returns the wavelength axis, 'wl<-' sets it. |
wlconv |
Convert different wavelength units |
write.txt.long |
Import and Export of hyperSpec objects Besides 'save' and 'load', two general ways to import and export data into 'hyperSpec' objects exist. |
write.txt.wide |
Import and Export of hyperSpec objects Besides 'save' and 'load', two general ways to import and export data into 'hyperSpec' objects exist. |
!=-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 |
.DollarNames |
command line completion for $ |
.DollarNames-method |
command line completion for $ |
.DollarNames.hyperSpec |
command line completion for $ |
/-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 |