Welcome to hyperSpec! hyperSpec is a R package to handle hyperspectral data, i.e. spectra plus further information such as spatial information, time, concentrations, etc. Such data are frequently encountered in Raman, IR, NIR, UV/VIS, NMR, mass spectroscopy, AAS / AES, ... hyperSpec acts as an interface for the convenient handling of the spectra. Chemometric data analysis is done by R and other R packages.

The package is publicly accessible from the SVN repository.

There is also a R-forge project summary page.

Installation

Inside R

• To install the latest stable version from CRAN, type in R:

  install.packages("hyperSpec")

• To install the latest nightly build (development version), type in R:

  install.packages("hyperSpec",repos="http://R-Forge.R-project.org")

From source or binary archives automatically built by r-forge (nightly build)

1. Download the appropriate file.
2. Install the package:
   R CMD INSTALL filename

From svn source

1. get an svn checkout using your favourite svn client program, or
   svn checkout svn://svn.r-forge.r-project.org/svnroot/hyperspec/pkg
2. Install the package:
   R CMD INSTALL pkg-directory
   where pkg-directory is the directory where the svn checkout went (default is ./pkg).

Via package built on my computer

1. Download the prebuilt .tar.gz source (2012-May-14).
   Windows users will probably need the compiled .zip archive (2012-Feb-01)
   Versions for r-devel: tar.gz (2012-Feb-01)
2. Install the package:
   R CMD INSTALL filename

Documentation

• The Wiki-page gives an overview and
• provdes also a list of frequently asked questions.
• hyperSpec comes with some pdf documentation (vignettes) in addition to the R help files:
  • Introduction: user manual written from a spectroscopist's point of view
  • fileio: Detailed discussion of import and export of spectra files,
    the zipped directory containing all data is needed to reproduce the vignette.
  • plotting: graphical manual: example plots together with the code to produce the plots
  • Example work-flow: calibration of quinine fluorescence emission: how to program import functions for other file formats, and how to set up a calibration.
  • Example work-flow: Unstable Laser Emission: working with time series, conversion of the spectral abscissa ("wavelength axis")
  • Example work-flow: Raman map of chondrocytes in cartilage: principal component analysis, cluster analysis, working with spectral maps/images.
    the zipped directory containing all data is needed to reproduce the vignette.
  • A more technical explanation of the baseline fitting technique used by spc.fit.poly.below

  In the standard hyperSpec installation, .pdf files and source are already available in the documentation directory, with the exception of the the chondrocyte and fileio raw data (see above).

Help, Suggestions, Feature Requests, and Bug Reports

• There is a help forum on hyperSpec
• and a discussion forum where suggestions for further development of hyperSpec can be discussed.
• The very low traffic mailing list hyperSpec-commits is used to announce major bug fixes and new features. Subscription, archives,and search are available.
• The mailing list hyperSpec-help discusses questions on the use of hyperSpec: subscribe, read the archives, or search
• Trackers for feature requests and
• bugs are also found on r-forge.

About hyperSpec

• Claudia Beleites, Christoph Krafft, Jürgen Popp & Valter Sergo:
  hyperSpec: working with spectroscopic data
  The R User Conference, useR! 2011 (oral presentation) 2011
• Claudia Beleites & Valter Sergo:
  Chemometric Analysis of Spectroscopic Data in R: hyperSpec
  13th ECSBM, XVth Euroanalysis, and FTIR-Workshop at RKI (poster) 2009
• Sebastian Mellor, Claudia Beleites, Colin Gillespie, Christoph Krafft & Jürgen Popp:
  Graphical Interaction in Spectrosopic Data Analysis: hyperSpecGUI
  The R User Conference, useR! 2011 (poster) 2011

Work using hyperSpec

• Claudia Beleites, Kathrin Geiger, Matthias Kirsch, Stephan B Sobottka, Gabriele Schackert & Reiner Salzer:
  Raman spectroscopic grading of astrocytoma tissues: using soft reference information.
  Anal Bioanal Chem, 2011, Vol. 400(9), pp. 2801-2816
• Claudia Beleites, Katrin Geiger, Gabriele Schackert, Reiner Salzer & Valter Sergo:
  Calculating Sensitivity and Specificity of Soft Classification Models
  Afrodata (oral presentation) 2010
• Claudia Beleites, Christoph Krafft, Jürgen Popp & Valter Sergo:
  Spectroscopic Data in R and Validation of Soft Classifiers: Classifying Cells and Tissues by Raman Spectroscopy
  The R User Conference, useR! 2011 (oral presentation) 2011
• Alois Bonifacio, Claudia Beleites, Franco Vittur, Eleonora Marsich, Sabrina Semeraro, Sergio Paoletti & Valter Sergo:
  Chemical imaging of articular cartilage sections with Raman mapping, employing uni- and multi-variate methods for data analysis.
  Analyst, 2010, Vol. 135(12), pp. 3193-3204

Contact

Claudia Beleites
Dept. of Spectroscopy and Microscopy,
IPHT Jena
e-mail: claudia dot beleites at ipht minus jena dot de