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.

AuthorClaudia Beleites
Date of publication2016-11-19 10:14:29
MaintainerClaudia Beleites <chemometrie@beleites.de>
LicenseGPL (>= 3)
Version0.98-20161118
http://hyperSpec.r-forge.r-project.org/

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

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

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