# Interface for hyperspectral data, i.e. spectra + meta info (spatial, time, concentration, ...)

## Documentation for package ‘hyperSpec’ version 0.98-20110927

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- 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 | log,-method
acos-method | log,-method
acosh-method | log,-method
aggregate | aggregate hyperSpec objects
aggregate-method | aggregate hyperSpec objects
all-method | The functions...
all.equal | all.equal,-method
all.equal-method | all.equal,-method
alois.palette | Matlab-like Palettes...
any-method | The functions...
apply | apply...
apply-method | apply...
Arith-method | Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%
as.character | as.character,hyperSpec-method
as.character-method | as.character,hyperSpec-method
as.data.frame | Conversion of a hyperSpec object into a data...
as.data.frame-method | Conversion of a hyperSpec object into a data...
as.data.frame-methods | Conversion of a hyperSpec object into a data...
as.long.df | Conversion of a hyperSpec object into a data...
as.matrix | Conversion of a hyperSpec object into a data...
as.matrix-method | Conversion of a hyperSpec object into a data...
as.matrix-methods | Conversion of a hyperSpec object into a data...
as.t.df | Conversion of a hyperSpec object into a data...
as.wide.df | Conversion of a hyperSpec object into a data...
asin-method | log,-method
asinh-method | log,-method
atan-method | log,-method
atanh-method | log,-method
ave-method | aggregate hyperSpec objects

## -- B --

barbiturates | Barbiturates Spectra from...
bind | Binding hyperSpec Objects...

## -- C --

cbind.hyperSpec | Binding hyperSpec Objects...
cbind2 | Binding hyperSpec Objects...
cbind2-method | Binding hyperSpec Objects...
ceiling-method | log,-method
chk.hy | Validation of hyperSpec objects
chondro | Raman spectra of 2 Chondrocytes in Cartilage...
collapse | Collapse hyperSpec objects
collapse.hyperSpec | Collapse hyperSpec objects
colnames | Dimnames for hyperSpec objects...
colnames-method | Dimnames for hyperSpec objects...
colnames<- | Dimnames for hyperSpec objects...
colnames<--method | Dimnames for hyperSpec objects...
Compare | all.equal,-method
Compare-method | all.equal,-method
Comparison | all.equal,-method
Comparison-method | all.equal,-method
cos-method | log,-method
cosh-method | log,-method
create | Creating a hyperSpec Object...
create-method | Creating a hyperSpec Object...
cummax-method | log,-method
cummin-method | log,-method
cumprod-method | log,-method
cumsum-method | log,-method

## -- D --

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

## -- E --

empty | Empty hyperSpec object...
exp-method | log,-method
expm1-method | log,-method
export | Import and Export of hyperSpec objects...

## -- F --

floor-method | log,-method
flu | Quinine Fluorescence Spectra...

## -- G --

gamma-method | log,-method

## -- H --

hy.getOption | Options for package hyperSpec...
hy.getOptions | Options for package hyperSpec...
hy.setOptions | Options for package hyperSpec...
hy.unittest | hyperSpec unit tests...
hyperSpec Arith | Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%
hyperSpec-class | Class "hyperSpec"

## -- I --

i2wl | Conversion between Wavelength and Spectra Matrix Column...
import | Import and Export of hyperSpec objects...
initialize | Creating a hyperSpec Object...
initialize-method | Creating a hyperSpec Object...
is.na | The functions...
is.na-method | The functions...
isample | Random Samples and Permutations...

## -- L --

labels | labels<-
labels-method | labels<-
labels<- | labels<-
laser | Laser Emission...
length | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an...
length-method | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an...
levelplot | levelplot,formula,hyperSpec-method
levelplot-method | levelplot,formula,hyperSpec-method
lgamma-method | log,-method
log | log,-method
log-method | log,-method
log1p-method | log,-method
logbook | Logging the processing ot a hyperSpec Object...
logentry | Append a Row to the logbook of a hyperSpec Object...

## -- M --

map.identify | levelplot,formula,hyperSpec-method
map.sel.poly | Interactively select a polygon (grid graphics) and highlight points...
mark.dendrogram | Mark groups in 'hclust' dendrograms
Math | log,-method
Math-method | log,-method
Math2 | log,-method
Math2-method | log,-method
matlab.dark.palette | Matlab-like Palettes...
matlab.palette | Matlab-like Palettes...
max-method | The functions...
mean | Mean and Standard Deviation...
mean-method | Mean and Standard Deviation...
mean_pm_sd | Mean and Standard Deviation...
mean_pm_sd-method | Mean and Standard Deviation...
mean_sd | Mean and Standard Deviation...
mean_sd-method | Mean and Standard Deviation...
merge | Merge hyperSpec objects...
merge-method | Merge hyperSpec objects...
min-method | The functions...

## -- N --

ncol | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an...
ncol-method | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an...
new | Creating a hyperSpec Object...
new-method | Creating a hyperSpec Object...
nrow | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an...
nrow-method | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an...
nwl | The Number of Rows (Spectra), Columns, and Data Points per Spectrum of an...

## -- O --

Operators | all.equal,-method
orderwl | Sorting the Wavelengths of a hyperSpec Object...

## -- P --

paracetamol | Paracetamol Spectrum...
pearson.dist | Distance based on Pearson's R^2R squared...
plot | Plotting hyperSpec Objects...
plot-method | Plotting hyperSpec Objects...
plot-methods | Plotting hyperSpec Objects...
plot-methods-method | Plotting hyperSpec Objects...
plotc | Calibration- and Timeseries Plots, Depth-Profiles and the like...
plotmap | levelplot,formula,hyperSpec-method
plotspc | Plotting Spectra...
plotvoronoi | levelplot,formula,hyperSpec-method
print | as.character,hyperSpec-method
print-method | as.character,hyperSpec-method
prod-method | The functions...

## -- Q --

qplotc | Spectra plotting with ggplot2
qplotmap | Spectra plotting with ggplot2
qplotspc | Spectra plotting with ggplot2
quantile | Mean and Standard Deviation...
quantile-method | Mean and Standard Deviation...

## -- R --

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 | Binding hyperSpec Objects...
rbind2-method | Binding hyperSpec Objects...
read.ENVI | read.ENVI.Nicolet
read.ENVI.Nicolet | read.ENVI.Nicolet
read.spc | read.spc.KaiserMap
read.spc.KaiserMap | read.spc.KaiserMap
read.txt.long | Import and Export of hyperSpec objects...
read.txt.wide | Import and Export of hyperSpec objects...
round-method | log,-method
rownames | Dimnames for hyperSpec objects...
rownames-method | Dimnames for hyperSpec objects...
rownames<- | Dimnames for hyperSpec objects...
rownames<--method | Dimnames for hyperSpec objects...

## -- S --

sample | Random Samples and Permutations...
sample-method | Random Samples and Permutations...
scan.txt.Renishaw | import Raman measurements from Renishaw ASCII-files...
scan.txt.Witec | File Import Witec Raman
scan.zip.Renishaw | import Raman measurements from Renishaw ASCII-files...
sel.poly | Interactively select a polygon (grid graphics)...
seq-method | Sequence generation along spectra or wavelengths...
seq.hyperSpec | Sequence generation along spectra or wavelengths...
show | as.character,hyperSpec-method
show-method | as.character,hyperSpec-method
sign-method | log,-method
signif-method | log,-method
sin-method | log,-method
sinh-method | log,-method
spc.bin | Wavelength Binning...
spc.fit.poly | Polynomial Baseline Fitting...
spc.fit.poly.below | Polynomial Baseline Fitting...
spc.identify | Identifying Spectra and Spectral Data Points...
spc.label.default | Identifying Spectra and Spectral Data Points...
spc.label.wlonly | Identifying Spectra and Spectral Data Points...
spc.loess | loess smoothing interpolation for spectra...
spc.NA.linapprox | Impute missing data points...
spc.point.default | Identifying Spectra and Spectral Data Points...
spc.point.max | Identifying Spectra and Spectral Data Points...
spc.point.min | Identifying Spectra and Spectral Data Points...
spc.point.sqr | Identifying Spectra and Spectral Data Points...
split | Split a hyperSpec object according to groups...
split-method | Split a hyperSpec object according to groups...
split-methods | Split a hyperSpec object according to groups...
sqrt-method | log,-method
stacked.offsets | Plotting Spectra...
sum-method | The functions...
Summary | The functions...
summary | as.character,hyperSpec-method
Summary-method | The functions...
summary-method | as.character,hyperSpec-method
sweep | Sweep Summary Statistic out of an hyperSpec Object...
sweep-method | Sweep Summary Statistic out of an hyperSpec Object...
sweep-methods | Sweep Summary Statistic out of an hyperSpec Object...

## -- T --

tan-method | log,-method
tanh-method | log,-method
trellis.factor.key | Color coding legend for factors...
trigamma-method | log,-method
trunc-method | log,-method

## -- V --

validObject | Validation of hyperSpec objects
validObject-method | Validation of hyperSpec objects

## -- W --

wc | wc...
wl | Getting and Setting the Wavelength Axis...
wl2i | Conversion between Wavelength and Spectra Matrix Column...
wl<- | Getting and Setting the Wavelength Axis...
write.txt.long | Import and Export of hyperSpec objects...
write.txt.wide | Import and Export of hyperSpec objects...

## -- misc --

!=-method | all.equal,-method
$ | 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: +, -, *, /, ^, %%, %/%, %*%
%*% | Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%
%*%-method | Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%
%/%-method | Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%
*-method | Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%
+-method | Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%
--method | Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%
.DollarNames.hyperSpec | command line completion for $
/-method | Arithmetical Operators: +, -, *, /, ^, %%, %/%, %*%
<-method | all.equal,-method
<=-method | all.equal,-method
==-method | all.equal,-method
>-method | all.equal,-method
>=-method | all.equal,-method
[ | 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: +, -, *, /, ^, %%, %/%, %*%