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

Comfortable ways to work with hyperspectral data sets. I.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f (wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.

Install the latest version of this package by entering the following in R:
AuthorClaudia Beleites
Date of publication2016-11-19 10:14:29
MaintainerClaudia Beleites <chemometrie@beleites.de>
LicenseGPL (>= 3)

View on CRAN

Man pages

aggregate: aggregate hyperSpec objects

apply: apply Computes summary statistics for the spectra of a...

Arith: Arithmetical Operators for hyperSpec objects

asdataframe: Conversion of a hyperSpec object into a data.frame or matrix...

barbiturates: Barbiturates Spectra from .spc example files A time series of...

baselines: Polynomial Baseline Fitting These functions fit polynomal...

bind: Binding hyperSpec Objects Two S3 functions 'cbind.hyperSpec'...

chk.hy: Validation of hyperSpec objects

chondro: Raman spectra of 2 Chondrocytes in Cartilage A Raman-map...

collapse: Collapse hyperSpec objects

colSums: colSums, colMeans, rowSums and rowMeans functions for...

Comparison: Comparison of hyperSpec objects

cov: Covariance matrices for hyperSpec objects

decomposition: Convert Principal Component Decomposition or the like into a...

dim: The Number of Rows (Spectra), Columns, and Data Points per...

dimnames: dimnames for hyperSpec objects

dollarnames: command line completion for $

empty: Empty hyperSpec object

extractreplace: Extract and Replace parts of hyperSpec objects

flu: Quinine Fluorescence Spectra Fluorescence spectra of...

hyperSpec-class: Class "hyperSpec" This class handles hyperspectral data sets,...

hyperSpec-package: Package hyperSpec

initialize: Creating a hyperSpec Object Like other S4 objects, a...

labels: Get and Set Labels of a hyperSpec Object 'value' may be a...

laser: Laser Emission A time series of an unstable laser emission.

levelplot: Plot a Map and Identify/Select Spectra in the Map 'levelplot'...

makeraster: makeraster

map-sel-poly: Interactively select a polygon (grid graphics) and highlight...

mark.dendrogram: Mark groups in 'hclust' dendrograms

markpeak: Mark peak Marks location of the _first_ spectrum at the data...

math: Math Functions for hyperSpec Objects

mean_sd: Mean and Standard Deviation Calculate mean and standard...

merge: Merge hyperSpec objects

normalize01: normalization for mixed colors

options: Options for package hyperSpec Functions to access and set...

orderwl: Sorting the Wavelengths of a hyperSpec Object Rearranges the...

palettes: Matlab-like Palettes Two palettes going from blue over green...

paracetamol: Paracetamol Spectrum A Raman spectrum of a paracetamol...

pearson.dist: Distance based on Pearson's R squared

plot: Plotting hyperSpec Objects

plotc: Calibration- and Timeseries Plots, Depth-Profiles and the...

plotmat: Plot spectra matrix

plotspc: Plotting Spectra Plot the spectra of a 'hyperSpec' object,...

qplotc: Spectra plotting with ggplot2

qplotmap: Spectra plotting with ggplot2

qplotmix: Plot multivariate data into colour channels

qplotmixmap: qplotmap with colour mixing for multivariate overlay

qplotspc: Spectra plotting with ggplot2

quickdf: Quick data frame. Experimental version of 'as.data.frame'...

rbind-fill: Bind matrices by row, and fill missing columns with NA

read.ENVI: 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...

read-spc-Kaiser: read Kaiser .spc files

read.spe: Import WinSpec SPE file

read.txt.Horiba: Import Horiba Labspec exported ASCII files

read.txt.Shimadzu: Reads Shimadzu GCxGC-qMS - Spectra Files (.txt) as exported...

rmmvnorm: Multivariate normal random numbers

sample: Random Samples and Permutations Take a sample of the...

scale: Center and scale hyperSpec object

scan.asc.Andor: File Import Andor Solis

scan-txt-Renishaw: import Raman measurements from Renishaw ASCII-files import...

scan.txt.Witec: File Import Witec Raman

seq: Sequence generation along spectra or wavelengths This...

show: Convert a hyperSpec object to character strings for Display...

spc-bin: Wavelength Binning In order to reduce the spectral resolution...

spc-identify: Identifying Spectra and Spectral Data Points This function...

spc-loess: loess smoothing interpolation for spectra Spectra can be...

spc.NA.linapprox: Impute missing data points

spc-rubberband: Rubberband baseline correction

spc-spline: Spectral smoothing by splines

split: Split a hyperSpec object according to groups 'split' divides...

subset: subset

summary: The functions

sweep: Sweep Summary Statistic out of an hyperSpec Object 'sweep'...

textio: Import and Export of hyperSpec objects Besides 'save' and...

trellis.factor.key: Color coding legend for factors Modifies a list of lattice...

unittests: hyperSpec unit tests If 'svUnit' is available, run the unit...

vanderMonde: Function evaluation on hyperSpec objects

wc: wc word count of ASCII files

wl: Getting and Setting the Wavelength Axis 'wl' returns the...

wl2i: Conversion between Wavelength and Spectra Matrix Column Index...

wlconv: Convert different wavelength units

wl.eval: Evaluate function on wavelengths of hyperSpec object


[ Man page
[<- Man page
[[ Man page
[[<- Man page
$ Man page
$<- Man page
\%*\% Man page
abs,hyperSpec-method Man page
acosh,hyperSpec-method Man page
acos,hyperSpec-method Man page
aggregate Man page
aggregate,hyperSpec-method Man page
all.equal Man page
all.equal,hyperSpec,hyperSpec-method Man page
all,hyperSpec-method Man page
alois.palette Man page
any,hyperSpec-method Man page
apply Man page
apply,hyperSpec-method Man page
Arith Man page
Arith,hyperSpec,hyperSpec-method Man page
Arith,hyperSpec,matrix-method Man page
Arith,hyperSpec-method Man page
Arith,hyperSpec,missing-method Man page
Arith,hyperSpec,numeric-method Man page
Arith,matrix,hyperSpec-method Man page
Arith,numeric,hyperSpec-method Man page
as.character Man page
as.character,hyperSpec-method Man page
as.data.frame Man page
as.data.frame.hyperSpec Man page
as.data.frame,hyperSpec-method Man page
asinh,hyperSpec-method Man page
asin,hyperSpec-method Man page
as.long.df Man page
as.matrix Man page
as.matrix.hyperSpec Man page
as.matrix,hyperSpec-method Man page
as.t.df Man page
as.wide.df Man page
atanh,hyperSpec-method Man page
atan,hyperSpec-method Man page
ave,hyperSpec-method Man page
barbiturates Man page
bind Man page
cbind2,hyperSpec,hyperSpec-method Man page
cbind2,hyperSpec,missing-method Man page
cbind.hyperSpec Man page
ceiling,hyperSpec-method Man page
chk.hy Man page
chondro Man page
collapse Man page
collapse.hyperSpec Man page
colMeans,hyperSpec-method Man page
colmix.rgb Man page
colnames Man page
colnames<- Man page
colnames<-,hyperSpec-method Man page
colnames,hyperSpec-method Man page
colSums Man page
colSums,hyperSpec-method Man page
Compare,hyperSpec,hyperSpec-method Man page
Compare,hyperSpec,matrix-method Man page
Compare,hyperSpec-method Man page
Compare,hyperSpec,numeric-method Man page
Compare,matrix,hyperSpec-method Man page
Compare,numeric,hyperSpec-method Man page
Comparison Man page
cosh,hyperSpec-method Man page
cos,hyperSpec-method Man page
cov,hyperSpec,missing-method Man page
create Man page
create,hyperSpec-method Man page
cummax,hyperSpec-method Man page
cummin,hyperSpec-method Man page
cumprod,hyperSpec-method Man page
cumsum,hyperSpec-method Man page
decomposition Man page
digamma,hyperSpec-method Man page
dim,hyperSpec-method Man page
dimnames Man page
dimnames,hyperSpec-method Man page
.DollarNames Man page
.DollarNames.hyperSpec Man page
.DollarNames,hyperSpec-method Man page
empty Man page
ev2freq Man page
ev2invcm Man page
ev2nm Man page
ev2raman Man page
exp,hyperSpec-method Man page
expm1,hyperSpec-method Man page
export Man page
fitraster Man page
floor,hyperSpec-method Man page
flu Man page
freq2ev Man page
freq2invcm Man page
freq2nm Man page
freq2raman Man page
gamma,hyperSpec-method Man page
hy.getOption Man page
hy.getOptions Man page
hyperSpec-class Man page
^,hyperSpec,hyperSpec-method Man page
<=,hyperSpec,hyperSpec-method Man page
<,hyperSpec,hyperSpec-method Man page
==,hyperSpec,hyperSpec-method Man page
>=,hyperSpec,hyperSpec-method Man page
>,hyperSpec,hyperSpec-method Man page
-,hyperSpec,hyperSpec-method Man page
!=,hyperSpec,hyperSpec-method Man page
/,hyperSpec,hyperSpec-method Man page
*,hyperSpec,hyperSpec-method Man page
\%/\%,hyperSpec,hyperSpec-method Man page
\%*\%,hyperSpec,hyperSpec-method Man page
\%\%,hyperSpec,hyperSpec-method Man page
+,hyperSpec,hyperSpec-method Man page
\%*\%,hyperSpec,matrix-method Man page
[<-,hyperSpec-method Man page
[,hyperSpec-method Man page
[[<-,hyperSpec-method Man page
[[,hyperSpec-method Man page
$<-,hyperSpec-method Man page
$,hyperSpec-method Man page
hyperSpec-package Man page
hy.setOptions Man page
hy.unittest Man page
i2wl Man page
import Man page
initialize Man page
initialize,hyperSpec-method Man page
invcm2ev Man page
invcm2freq Man page
invcm2nm Man page
invcm2raman Man page
isample Man page
is.na,hyperSpec-method Man page
labels<- Man page
labels<-,hyperSpec-method Man page
labels,hyperSpec-method Man page
laser Man page
legendright Man page
length,hyperSpec-method Man page
levelplot,formula,hyperSpec-method Man page
levelplot,hyperSpec,missing-method Man page
lgamma,hyperSpec-method Man page
log Man page
log1p,hyperSpec-method Man page
log,hyperSpec-method Man page
makeraster Man page
map.identify Man page
map.sel.poly Man page
mark.dendrogram Man page
markpeak Man page
Math Man page
Math2 Man page
Math2,hyperSpec-method Man page
Math,hyperSpec-method Man page
matlab.dark.palette Man page
matlab.palette Man page
\%*\%,matrix,hyperSpec-method Man page
max,hyperSpec-method Man page
mean,hyperSpec-method Man page
mean_pm_sd Man page
mean_pm_sd,hyperSpec-method Man page
mean_pm_sd,matrix-method Man page
mean_pm_sd,numeric-method Man page
mean_sd Man page
mean_sd,hyperSpec-method Man page
mean_sd,matrix-method Man page
mean_sd,numeric-method Man page
merge Man page
merge,hyperSpec,hyperSpec-method Man page
min,hyperSpec-method Man page
ncol,hyperSpec-method Man page
new Man page
new,hyperSpec-method Man page
nm2ev Man page
nm2freq Man page
nm2invcm Man page
nm2raman Man page
normalize01 Man page
normalize01,hyperSpec-method Man page
normalize01,matrix-method Man page
normalize01,numeric-method Man page
normalize.colrange Man page
normalize.minmax Man page
normalize.null Man page
normalize.range Man page
nrow,hyperSpec-method Man page
nwl Man page
Operators Man page
orderwl Man page
paracetamol Man page
pearson.dist Man page
plot Man page
plot,ANY,ANY-method Man page
plotc Man page
plot,hyperSpec,character-method Man page
plot,hyperSpec,missing-method Man page
plotmap Man page
plotmat Man page
plot-methods Man page
plotspc Man page
plotvoronoi Man page
pooled.cov Man page
print Man page
print,hyperSpec-method Man page
prod,hyperSpec-method Man page
qmixlegend Man page
qmixtile Man page
qplotc Man page
qplotmap Man page
qplotmixmap Man page
qplotspc Man page
quantile,hyperSpec-method Man page
quickdf Man page
raman2ev Man page
raman2freq Man page
raman2invcm Man page
raman2nm Man page
range,hyperSpec-method Man page
rbind2,hyperSpec,hyperSpec-method Man page
rbind2,hyperSpec,missing-method Man page
rbind.fill Man page
rbind.fill.matrix Man page
rbind.hyperSpec Man page
read.cytomat Man page
read.ENVI Man page
read.ENVI.Nicolet Man page
read.ini Man page
read.jdx Man page
read.jdx.Shimadzu Man page
read.mat.Cytospec Man page
read.spc Man page
read.spc.Kaiser Man page
read.spc.KaiserLowHigh Man page
read.spc.KaiserMap Man page
read.spe Man page
read.spe.header Man page
read.txt.Horiba Man page
read.txt.Horiba.t Man page
read.txt.Horiba.xy Man page
read.txt.long Man page
read.txt.Shimadzu Man page
read.txt.wide Man page
rmmvnorm Man page
rmmvnorm,hyperSpec-method Man page
rmmvnorm,numeric,hyperSpec,array-method Man page
rmmvnorm,numeric,hyperSpec,matrix-method Man page
rmmvnorm,numeric,matrix,array-method Man page
rmmvnorm,numeric,matrix,matrix-method Man page
round,hyperSpec-method Man page
rowMeans,hyperSpec-method Man page
rownames Man page
rownames<- Man page
rownames<-,hyperSpec-method Man page
rownames,hyperSpec-method Man page
rowSums,hyperSpec-method Man page
sample,data.frame-method Man page
sample,hyperSpec-method Man page
sample,matrix-method Man page
scale Man page
scale,hyperSpec-method Man page
scale-methods Man page
scan.asc.Andor Man page
scan.dat.Witec Man page
scan.txt.Renishaw Man page
scan.txt.Witec Man page
scan.txt.Witec.Graph Man page
scan.zip.Renishaw Man page
sel.poly Man page
seq Man page
seq.hyperSpec Man page
seq,hyperSpec-method Man page
show Man page
show,hyperSpec-method Man page
sign,hyperSpec-method Man page
signif,hyperSpec-method Man page
sinh,hyperSpec-method Man page
sin,hyperSpec-method Man page
spc.bin Man page
spc.fit.poly Man page
spc.fit.poly.below Man page
spc.identify Man page
spc.label.default Man page
spc.label.wlonly Man page
spc.loess Man page
spc.NA.linapprox Man page
spc.point.default Man page
spc.point.max Man page
spc.point.min Man page
spc.point.sqr Man page
spc.rubberband Man page
spc.smooth.spline Man page
spe.showcalpoints Man page
split Man page
split,ANY-method Man page
split,hyperSpec-method Man page
split-methods Man page
sqrt,hyperSpec-method Man page
stacked.offsets Man page
subset Man page
subset,hyperSpec-method Man page
sum,hyperSpec-method Man page
summary Man page
Summary Man page
summary,hyperSpec-method Man page
Summary,hyperSpec-method Man page
sweep Man page
sweep,hyperSpec-method Man page
sweep-methods Man page
tanh,hyperSpec-method Man page
tan,hyperSpec-method Man page
trellis.factor.key Man page
trigamma,hyperSpec-method Man page
trunc,hyperSpec-method Man page
validObject Man page
validObject,hyperSpec-method Man page
vanderMonde Man page
vanderMonde,hyperSpec-method Man page
wc Man page
wl Man page
wl<- Man page
wl2i Man page
wlconv Man page
wl.eval Man page
write.txt.long Man page
write.txt.wide Man page


tests/testthat/test-plotspc.r tests/testthat/test-stacked.offsets.r tests/testthat/test-collapse.r
R/write.txt.wide.R R/decomposition.R R/wl.R R/scale.R R/spc.bin.R R/plotvoronoi.R R/trellis.factor.key.R R/chk.hy.R R/scan.txt.Renishaw.R R/dimnames.R R/spc.loess.R R/scan.txt.Witec.R R/quantile.R R/empty.R R/seq.R R/subset.R R/hyperspec-package.R R/vandermonde.R R/all.equal.R R/qplot.R R/aggregate.R R/pearson.dist.R R/dim.R R/flu.R R/plot.R R/cov.R R/fileio.optional.R R/factor2num.R R/mean_sd.R R/chondro.R R/read.mat.Witec.R R/map.identify.R R/read.jdx.R R/y-pastenames.R R/scan.asc.Andor.R R/sample.R R/spc.identify.R
R/call.list.R R/makeraster.R R/initialize.R R/laser.R R/normalize01.R R/read.ENVI.R R/show.R R/wl2i.R R/qplotmixmap.R R/plotmat.R R/replace.R R/plotspc.R R/wc.R R/split.string.R R/read.txt.wide.R R/mvtnorm.R R/spc.rubberband.R R/read.spc.Kaiser.R R/spc.fit.poly.R R/barbiturates.R R/options.R R/levelplot.R R/read.spc.R R/write.txt.long.R R/bind.R R/apply.R R/orderwl.R R/read.jdx.Shimadzu.R R/matlab.palette.R R/as.data.frame.R R/rbind.fill.R R/read.spe.R R/getbynames.R R/unittest.R R/units.R R/spc.NA.approx.R R/split.R R/labels.R R/paracetamol.R R/mark.peak.R R/read.ini.R R/hyperspec-class.R R/mark.dendrogram.R R/map.sel.poly.R R/read.mat.Cytospec.R R/wleval.R R/extract.R R/colMeans.R R/paste.row.R R/Math.R R/collapse.R R/splitdots.R R/sweep.R R/merge.R R/plotc.R R/read.txt.Shimadzu.R R/read.txt.Horiba.R R/DollarNames.R R/Compare.R R/validate.R R/spc.spline.R R/Summary.R R/zzz.R R/plotmap.R R/read.txt.long.R R/read.ENVI.Nicolet.R R/Arith.R
man/chk.hy.Rd man/spc-spline.Rd man/normalize01.Rd man/read.mat.Cytospec.Rd man/spc-rubberband.Rd man/markpeak.Rd man/unittests.Rd man/show.Rd man/scale.Rd man/mark.dendrogram.Rd man/math.Rd man/laser.Rd man/pearson.dist.Rd man/paracetamol.Rd man/cov.Rd man/orderwl.Rd man/asdataframe.Rd man/colSums.Rd man/qplotc.Rd man/read.ENVI.Rd man/baselines.Rd man/flu.Rd man/spc.NA.linapprox.Rd man/plotmat.Rd man/bind.Rd man/read-spc-Kaiser.Rd man/quickdf.Rd man/hyperSpec-package.Rd man/wl.Rd man/read-ini.Rd man/merge.Rd man/makeraster.Rd man/aggregate.Rd man/scan.txt.Witec.Rd man/read.txt.Shimadzu.Rd man/textio.Rd man/extractreplace.Rd man/split.Rd man/rbind-fill.Rd man/empty.Rd man/wc.Rd man/chondro.Rd man/options.Rd man/labels.Rd man/Arith.Rd man/read-spc.Rd man/decomposition.Rd man/Comparison.Rd man/spc-identify.Rd man/qplotmap.Rd man/qplotmixmap.Rd man/map-sel-poly.Rd man/plotc.Rd man/mean_sd.Rd man/scan.asc.Andor.Rd man/read.jdx.Rd man/plotspc.Rd man/qplotspc.Rd man/levelplot.Rd man/sweep.Rd man/rmmvnorm.Rd man/collapse.Rd man/dollarnames.Rd man/apply.Rd man/initialize.Rd man/seq.Rd man/spc-loess.Rd man/dimnames.Rd man/dim.Rd man/plot.Rd man/trellis.factor.key.Rd man/sample.Rd man/read.spe.Rd man/wl2i.Rd man/subset.Rd man/wl.eval.Rd man/read.txt.Horiba.Rd man/summary.Rd man/hyperSpec-class.Rd man/spc-bin.Rd man/vanderMonde.Rd man/wlconv.Rd man/qplotmix.Rd man/palettes.Rd man/barbiturates.Rd man/scan-txt-Renishaw.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.