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

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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.

Author
Claudia Beleites
Date of publication
2016-11-19 10:14:29
Maintainer
Claudia Beleites <chemometrie@beleites.de>
License
GPL (>= 3)
Version
0.98-20161118
URLs

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

Files in this package

hyperSpec
hyperSpec/inst
hyperSpec/inst/CITATION
hyperSpec/inst/doc
hyperSpec/inst/doc/plotting.R
hyperSpec/inst/doc/chondro.Rnw
hyperSpec/inst/doc/fileio.Rnw
hyperSpec/inst/doc/flu.R
hyperSpec/inst/doc/laser.Rnw
hyperSpec/inst/doc/laser.R
hyperSpec/inst/doc/introduction.Rnw
hyperSpec/inst/doc/rawdata
hyperSpec/inst/doc/rawdata/laser.txt.gz
hyperSpec/inst/doc/rawdata/flu3.txt
hyperSpec/inst/doc/rawdata/flu5.txt
hyperSpec/inst/doc/rawdata/flu2.txt
hyperSpec/inst/doc/rawdata/flu1.txt
hyperSpec/inst/doc/rawdata/flu4.txt
hyperSpec/inst/doc/rawdata/flu6.txt
hyperSpec/inst/doc/introduction.R
hyperSpec/inst/doc/baseline.Rnw
hyperSpec/inst/doc/laserdata
hyperSpec/inst/doc/fileio.pdf
hyperSpec/inst/doc/introduction.pdf
hyperSpec/inst/doc/vignettes.defs
hyperSpec/inst/doc/plotting.pdf
hyperSpec/inst/doc/plotting.Rnw
hyperSpec/inst/doc/scan.txt.PerkinElmer.R
hyperSpec/inst/doc/flu.Rnw
hyperSpec/inst/doc/laser.pdf
hyperSpec/inst/doc/flu.pdf
hyperSpec/inst/doc/chondro.pdf
hyperSpec/inst/doc/baseline.pdf
hyperSpec/inst/doc/baseline.R
hyperSpec/tests
hyperSpec/tests/test.spc
hyperSpec/tests/interactive.tests
hyperSpec/tests/unittests.Rout
hyperSpec/tests/unittests.R
hyperSpec/tests/testthat
hyperSpec/tests/testthat/test-plotspc.r
hyperSpec/tests/testthat/test-stacked.offsets.r
hyperSpec/tests/testthat/test-collapse.r
hyperSpec/NAMESPACE
hyperSpec/data
hyperSpec/data/flu.rda
hyperSpec/data/laser.rda
hyperSpec/data/barbiturates.rda
hyperSpec/data/paracetamol.rda
hyperSpec/R
hyperSpec/R/write.txt.wide.R
hyperSpec/R/decomposition.R
hyperSpec/R/wl.R
hyperSpec/R/scale.R
hyperSpec/R/spc.bin.R
hyperSpec/R/plotvoronoi.R
hyperSpec/R/trellis.factor.key.R
hyperSpec/R/chk.hy.R
hyperSpec/R/scan.txt.Renishaw.R
hyperSpec/R/dimnames.R
hyperSpec/R/spc.loess.R
hyperSpec/R/scan.txt.Witec.R
hyperSpec/R/quantile.R
hyperSpec/R/empty.R
hyperSpec/R/seq.R
hyperSpec/R/subset.R
hyperSpec/R/hyperspec-package.R
hyperSpec/R/vandermonde.R
hyperSpec/R/all.equal.R
hyperSpec/R/qplot.R
hyperSpec/R/aggregate.R
hyperSpec/R/pearson.dist.R
hyperSpec/R/dim.R
hyperSpec/R/flu.R
hyperSpec/R/plot.R
hyperSpec/R/cov.R
hyperSpec/R/fileio.optional.R
hyperSpec/R/factor2num.R
hyperSpec/R/mean_sd.R
hyperSpec/R/chondro.R
hyperSpec/R/read.mat.Witec.R
hyperSpec/R/map.identify.R
hyperSpec/R/read.jdx.R
hyperSpec/R/y-pastenames.R
hyperSpec/R/scan.asc.Andor.R
hyperSpec/R/sample.R
hyperSpec/R/spc.identify.R
hyperSpec/R/sysdata.rda
hyperSpec/R/call.list.R
hyperSpec/R/makeraster.R
hyperSpec/R/initialize.R
hyperSpec/R/laser.R
hyperSpec/R/normalize01.R
hyperSpec/R/read.ENVI.R
hyperSpec/R/show.R
hyperSpec/R/wl2i.R
hyperSpec/R/qplotmixmap.R
hyperSpec/R/plotmat.R
hyperSpec/R/replace.R
hyperSpec/R/plotspc.R
hyperSpec/R/wc.R
hyperSpec/R/split.string.R
hyperSpec/R/read.txt.wide.R
hyperSpec/R/mvtnorm.R
hyperSpec/R/spc.rubberband.R
hyperSpec/R/read.spc.Kaiser.R
hyperSpec/R/spc.fit.poly.R
hyperSpec/R/barbiturates.R
hyperSpec/R/options.R
hyperSpec/R/levelplot.R
hyperSpec/R/read.spc.R
hyperSpec/R/write.txt.long.R
hyperSpec/R/bind.R
hyperSpec/R/apply.R
hyperSpec/R/orderwl.R
hyperSpec/R/read.jdx.Shimadzu.R
hyperSpec/R/matlab.palette.R
hyperSpec/R/as.data.frame.R
hyperSpec/R/rbind.fill.R
hyperSpec/R/read.spe.R
hyperSpec/R/getbynames.R
hyperSpec/R/unittest.R
hyperSpec/R/units.R
hyperSpec/R/spc.NA.approx.R
hyperSpec/R/split.R
hyperSpec/R/labels.R
hyperSpec/R/paracetamol.R
hyperSpec/R/mark.peak.R
hyperSpec/R/read.ini.R
hyperSpec/R/hyperspec-class.R
hyperSpec/R/mark.dendrogram.R
hyperSpec/R/map.sel.poly.R
hyperSpec/R/read.mat.Cytospec.R
hyperSpec/R/wleval.R
hyperSpec/R/extract.R
hyperSpec/R/colMeans.R
hyperSpec/R/paste.row.R
hyperSpec/R/Math.R
hyperSpec/R/collapse.R
hyperSpec/R/splitdots.R
hyperSpec/R/sweep.R
hyperSpec/R/merge.R
hyperSpec/R/plotc.R
hyperSpec/R/read.txt.Shimadzu.R
hyperSpec/R/read.txt.Horiba.R
hyperSpec/R/DollarNames.R
hyperSpec/R/Compare.R
hyperSpec/R/validate.R
hyperSpec/R/spc.spline.R
hyperSpec/R/Summary.R
hyperSpec/R/zzz.R
hyperSpec/R/plotmap.R
hyperSpec/R/read.txt.long.R
hyperSpec/R/read.ENVI.Nicolet.R
hyperSpec/R/Arith.R
hyperSpec/vignettes
hyperSpec/vignettes/chondro.Rnw
hyperSpec/vignettes/functions.RData
hyperSpec/vignettes/fileio.Rnw
hyperSpec/vignettes/laser.Rnw
hyperSpec/vignettes/.install_extras
hyperSpec/vignettes/introduction.Rnw
hyperSpec/vignettes/rawdata
hyperSpec/vignettes/rawdata/laser.txt.gz
hyperSpec/vignettes/rawdata/flu3.txt
hyperSpec/vignettes/rawdata/flu5.txt
hyperSpec/vignettes/rawdata/flu2.txt
hyperSpec/vignettes/rawdata/flu1.txt
hyperSpec/vignettes/rawdata/flu4.txt
hyperSpec/vignettes/rawdata/flu6.txt
hyperSpec/vignettes/baseline.Rnw
hyperSpec/vignettes/introduction.bib
hyperSpec/vignettes/vignettes.defs
hyperSpec/vignettes/plotting.Rnw
hyperSpec/vignettes/scan.txt.PerkinElmer.R
hyperSpec/vignettes/flu.Rnw
hyperSpec/vignettes/strukturhyperspec.pdf
hyperSpec/MD5
hyperSpec/build
hyperSpec/build/vignette.rds
hyperSpec/DESCRIPTION
hyperSpec/man
hyperSpec/man/chk.hy.Rd
hyperSpec/man/spc-spline.Rd
hyperSpec/man/normalize01.Rd
hyperSpec/man/read.mat.Cytospec.Rd
hyperSpec/man/spc-rubberband.Rd
hyperSpec/man/markpeak.Rd
hyperSpec/man/unittests.Rd
hyperSpec/man/show.Rd
hyperSpec/man/scale.Rd
hyperSpec/man/mark.dendrogram.Rd
hyperSpec/man/math.Rd
hyperSpec/man/laser.Rd
hyperSpec/man/pearson.dist.Rd
hyperSpec/man/paracetamol.Rd
hyperSpec/man/cov.Rd
hyperSpec/man/orderwl.Rd
hyperSpec/man/asdataframe.Rd
hyperSpec/man/colSums.Rd
hyperSpec/man/qplotc.Rd
hyperSpec/man/read.ENVI.Rd
hyperSpec/man/baselines.Rd
hyperSpec/man/flu.Rd
hyperSpec/man/spc.NA.linapprox.Rd
hyperSpec/man/plotmat.Rd
hyperSpec/man/bind.Rd
hyperSpec/man/read-spc-Kaiser.Rd
hyperSpec/man/quickdf.Rd
hyperSpec/man/hyperSpec-package.Rd
hyperSpec/man/wl.Rd
hyperSpec/man/read-ini.Rd
hyperSpec/man/merge.Rd
hyperSpec/man/makeraster.Rd
hyperSpec/man/aggregate.Rd
hyperSpec/man/scan.txt.Witec.Rd
hyperSpec/man/read.txt.Shimadzu.Rd
hyperSpec/man/textio.Rd
hyperSpec/man/extractreplace.Rd
hyperSpec/man/split.Rd
hyperSpec/man/rbind-fill.Rd
hyperSpec/man/empty.Rd
hyperSpec/man/wc.Rd
hyperSpec/man/chondro.Rd
hyperSpec/man/options.Rd
hyperSpec/man/labels.Rd
hyperSpec/man/Arith.Rd
hyperSpec/man/read-spc.Rd
hyperSpec/man/decomposition.Rd
hyperSpec/man/Comparison.Rd
hyperSpec/man/spc-identify.Rd
hyperSpec/man/qplotmap.Rd
hyperSpec/man/qplotmixmap.Rd
hyperSpec/man/map-sel-poly.Rd
hyperSpec/man/plotc.Rd
hyperSpec/man/mean_sd.Rd
hyperSpec/man/scan.asc.Andor.Rd
hyperSpec/man/read.jdx.Rd
hyperSpec/man/plotspc.Rd
hyperSpec/man/qplotspc.Rd
hyperSpec/man/levelplot.Rd
hyperSpec/man/sweep.Rd
hyperSpec/man/rmmvnorm.Rd
hyperSpec/man/collapse.Rd
hyperSpec/man/dollarnames.Rd
hyperSpec/man/apply.Rd
hyperSpec/man/initialize.Rd
hyperSpec/man/seq.Rd
hyperSpec/man/spc-loess.Rd
hyperSpec/man/dimnames.Rd
hyperSpec/man/dim.Rd
hyperSpec/man/plot.Rd
hyperSpec/man/trellis.factor.key.Rd
hyperSpec/man/sample.Rd
hyperSpec/man/read.spe.Rd
hyperSpec/man/wl2i.Rd
hyperSpec/man/subset.Rd
hyperSpec/man/wl.eval.Rd
hyperSpec/man/read.txt.Horiba.Rd
hyperSpec/man/summary.Rd
hyperSpec/man/hyperSpec-class.Rd
hyperSpec/man/spc-bin.Rd
hyperSpec/man/vanderMonde.Rd
hyperSpec/man/wlconv.Rd
hyperSpec/man/qplotmix.Rd
hyperSpec/man/palettes.Rd
hyperSpec/man/barbiturates.Rd
hyperSpec/man/scan-txt-Renishaw.Rd