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


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Documentation for package ‘hyperSpec’ version 0.98-20110927

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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: +, -, *, /, ^, %%, %/%, %*%