Last data update: 2014.03.03

hyperSpec

Package: hyperSpec
Type: Package
Title: Work with Hyperspectral Data, i.e. Spectra + Meta Information
(Spatial, Time, Concentration, ...)
Version: 0.98-20150304
Date: 2015-03-04
Author: Claudia Beleites
Maintainer: Claudia Beleites <chemometrie@beleites.de>
Description: 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.
License: GPL (>= 3)
LazyLoad: yes
LazyData: yes
Depends: R (>= 2.15), methods, utils, lattice, grid, ggplot2 (>=
0.9.2), mvtnorm
Suggests: R.matlab, tripack, deldir, rgl, plotrix, testthat, sp,
baseline, compiler, inline, Rcpp, MASS, fastcluster, pls
Imports: latticeExtra, svUnit
URL: http://hyperSpec.r-forge.r-project.org/
Collate: 'paste.row.R' 'paracetamol.R' 'laser.R' 'flu.R' 'chondro.R'
'barbiturates.R' 'hyperspec-package.R' 'validate.R'
'hyperspec-class.R' 'Arith.R' 'Compare.R' 'DollarNames.R'
'Math.R' 'Summary.R' 'aggregate.R' 'all.equal.R' 'apply.R'
'as.data.frame.R' 'bind.R' 'call.list.R' 'chk.hy.R'
'colMeans.R' 'collapse.R' 'cov.R' 'decomposition.R' 'dim.R'
'dimnames.R' 'empty.R' 'wl2i.R' 'extract.R' 'factor2num.R'
'fileio.optional.R' 'getbynames.R' 'initialize.R' 'labels.R'
'plotmap.R' 'levelplot.R' 'makeraster.R' 'map.identify.R'
'map.sel.poly.R' 'mark.dendrogram.R' 'matlab.palette.R'
'mean_sd.R' 'merge.R' 'mvtnorm.R' 'normalize01.R' 'options.R'
'orderwl.R' 'pearson.dist.R' 'plot.R' 'plotc.R' 'plotmat.R'
'plotspc.R' 'plotvoronoi.R' 'qplot.R' 'qplotmixmap.R'
'quantile.R' 'rbind.fill.R' 'read.ENVI.Nicolet.R' 'read.ENVI.R'
'read.cytomat.R' 'read.ini.R' 'read.jdx.R'
'read.jdx.Shimadzu.R' 'read.spc.Kaiser.R' 'read.spc.R'
'read.txt.Horiba.R' 'read.txt.Shimadzu.R' 'read.txt.long.R'
'read.txt.wide.R' 'replace.R' 'sample.R' 'scale.R'
'scan.txt.Renishaw.R' 'scan.txt.Witec.R' 'seq.R' 'show.R'
'spc.NA.approx.R' 'spc.bin.R' 'spc.fit.poly.R' 'spc.identify.R'
'spc.loess.R' 'spc.rubberband.R' 'spc.spline.R' 'split.R'
'split.string.R' 'splitdots.R' 'subset.R' 'sweep.R'
'trellis.factor.key.R' 'units.R' 'unittest.R' 'vandermonde.R'
'wc.R' 'wl.R' 'wleval.R' 'write.txt.long.R' 'write.txt.wide.R'
'y-pastenames.R' 'zzz.R'
Packaged: 2015-03-04 22:13:12 UTC; cb
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-05 07:17:32

● Cran Task View: ChemPhys
● 0 images, 77 functions, 5 datasets
● Reverse Depends: 0

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'hyperSpec' ...
** package 'hyperSpec' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'aggregate' from package 'stats' in package 'hyperSpec'
Creating a generic function for 'all.equal' from package 'base' in package 'hyperSpec'
Creating a generic function for 'apply' from package 'base' in package 'hyperSpec'
Creating a generic function for 'cov' from package 'stats' in package 'hyperSpec'
Creating a generic function for 'ncol' from package 'base' in package 'hyperSpec'
Creating a generic function for 'nrow' from package 'base' in package 'hyperSpec'
Creating a generic function for 'rownames' from package 'base' in package 'hyperSpec'
Creating a generic function for 'rownames<-' from package 'base' in package 'hyperSpec'
Creating a generic function for 'colnames' from package 'base' in package 'hyperSpec'
Creating a generic function for 'colnames<-' from package 'base' in package 'hyperSpec'
Creating a generic function for 'labels' from package 'base' in package 'hyperSpec'
Creating a generic function for 'mean' from package 'base' in package 'hyperSpec'
Creating a generic function for 'merge' from package 'base' in package 'hyperSpec'
Creating a generic function for 'quantile' from package 'stats' in package 'hyperSpec'
Creating a generic function for 'sample' from package 'base' in package 'hyperSpec'
Creating a generic function for 'scale' from package 'base' in package 'hyperSpec'
Creating a generic function for 'print' from package 'base' in package 'hyperSpec'
Creating a generic function for 'summary' from package 'base' in package 'hyperSpec'
Creating a generic function for 'split' from package 'base' in package 'hyperSpec'
Creating a generic function for 'subset' from package 'base' in package 'hyperSpec'
Creating a generic function for 'sweep' from package 'base' in package 'hyperSpec'
** help
*** installing help indices
  converting help for package 'hyperSpec'
    finding HTML links ... done
    Arith                                   html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/Arith.Rd:84: missing file link 'as.data.frame'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/Arith.Rd:97: missing file link 'sweep-methods'
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    Comparison                              html  
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    aggregate                               html  
    apply                                   html  
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    asdataframe                             html  
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    barbiturates                            html  
    baselines                               html  
    bind                                    html  
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    chk.hy                                  html  
    chondro                                 html  
    colSums                                 html  
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    collapse                                html  
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    cov                                     html  
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    decomposition                           html  
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    dim                                     html  
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    dimnames                                html  
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    dollarnames                             html  
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    empty                                   html  
    extractreplace                          html  
    flu                                     html  
    hyperSpec-class                         html  
    hyperSpec-package                       html  
    initialize                              html  
    labels                                  html  
    laser                                   html  
    levelplot                               html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/levelplot.Rd:80: missing file link 'panel.levelplot.raster'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/levelplot.Rd:98: missing file link 'panel.identify'
    makeraster                              html  
    map-sel-poly                            html  
    mark.dendrogram                         html  
    math                                    html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/math.Rd:91: missing file link 'Math'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/math.Rd:95: missing file link 'Summary'
    mean_sd                                 html  
    merge                                   html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/merge.Rd:16: missing file link 'merge.data.frame'
    normalize01                             html  
    options                                 html  
    orderwl                                 html  
    palettes                                html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/palettes.Rd:21: missing file link 'rainbow'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/palettes.Rd:22: missing file link 'colorRampPalette'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/palettes.Rd:42: missing file link 'rainbow'
    paracetamol                             html  
    pearson.dist                            html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/pearson.dist.Rd:35: missing file link 'as.dist'
    plot                                    html  
    plotc                                   html  
    plotmat                                 html  
    plotspc                                 html  
    qplotc                                  html  
    qplotmap                                html  
    qplotmix                                html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/qplotmix.Rd:47: missing file link 'colmix.rgb'
    qplotmixmap                             html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/qplotmixmap.Rd:12: missing file link 'qmixlegend'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/qplotmixmap.Rd:12: missing file link 'qmixtile'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/qplotmixmap.Rd:35: missing file link 'qmixtile'
    qplotspc                                html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/qplotspc.Rd:15: missing file link 'geom_line'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/qplotspc.Rd:17: missing file link 'geom_line'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/qplotspc.Rd:22: missing file link 'geom_line'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/qplotspc.Rd:51: missing file link 'geom_line'
    quickdf                                 html  
    rbind-fill                              html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/rbind-fill.Rd:79: missing file link 'rbind'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/rbind-fill.Rd:81: missing file link 'rbind'
    read-cytomat                            html  
    read-ini                                html  
    read-spc-Kaiser                         html  
    read-spc                                html  
    read.jdx                                html  
    read.txt.Horiba                         html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/read.txt.Horiba.Rd:21: missing file link 'read.txt.wide'
    read.txt.Shimadzu                       html  
    readENVI                                html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/readENVI.Rd:113: missing file link 'read.ENVI'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/readENVI.Rd:119: missing file link 'read.ENVI'
    rmmvnorm                                html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/rmmvnorm.Rd:31: missing file link 'rmvnorm'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/rmmvnorm.Rd:46: missing file link 'rmvnorm'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/rmmvnorm.Rd:48: missing file link 'pooled.cov'
    sample                                  html  
    scale                                   html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/scale.Rd:17: missing file link 'as.matrix'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/scale.Rd:22: missing file link 'as.matrix'
    scan-txt-Renishaw                       html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/scan-txt-Renishaw.Rd:40: missing file link 'gzfile'
    scan.dat.Witec                          html  
    seq                                     html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/seq.Rd:15: missing file link 'seq.int'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/seq.Rd:31: missing file link 'seq_along'
    show                                    html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/show.Rd:70: missing file link 'as.character'
    spc-bin                                 html  
    spc-identify                            html  
    spc-loess                               html  
    spc-rubberband                          html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/spc-rubberband.Rd:43: missing file link 'spc.fit.poly'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/spc-rubberband.Rd:43: missing file link 'spc.fit.poly.below'
    spc-spline                              html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/spc-spline.Rd:42: missing file link 'spc.loess'
    spc.NA.linapprox                        html  
    split                                   html  
    subset                                  html  
    summary                                 html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/summary.Rd:53: missing file link 'Summary'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/summary.Rd:55: missing file link 'isTRUE'
    sweep                                   html  
    textio                                  html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/textio.Rd:80: missing file link 'R.matlab'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/textio.Rd:88: missing file link 'read.spc'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/textio.Rd:90: missing file link 'read.ENVI'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/textio.Rd:104: missing file link 'R.matlab'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/textio.Rd:108: missing file link 'R.matlab'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/textio.Rd:116: missing file link 'read.spc'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/textio.Rd:118: missing file link 'read.ENVI'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/textio.Rd:131: missing file link 'R.matlab'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/textio.Rd:176: missing file link 'R.matlab'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/textio.Rd:178: missing file link 'read.ENVI'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/textio.Rd:180: missing file link 'read.spc'
    trellis.factor.key                      html  
    unittests                               html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/unittests.Rd:6: missing file link 'svUnit'
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    vanderMonde                             html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/vanderMonde.Rd:22: missing file link 'I'
    wc                                      html  
    wl                                      html  
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/wl.Rd:19: missing file link 'signif'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/wl.Rd:47: missing file link 'spc.loess'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/wl.Rd:48: missing file link 'spc.bin'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/wl.Rd:67: missing file link 'signif'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/wl.Rd:71: missing file link 'spc.loess'
Rd warning: /tmp/RtmplqsQBA/R.INSTALL2dc41f9669a3/hyperSpec/man/wl.Rd:73: missing file link 'spc.bin'
    wl.eval                                 html  
    wl2i                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hyperSpec)
Making 'packages.html' ... done

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO