baseline (version 1.3-5)

baseline-package: Baseline correction

Description

A common framework with implementations of several baseline correction methods

Author

Kristian Hovde Liland and Bjørn-Helge Mevik

Maintainer: Kristian Hovde Liland <[e-mail]>

Details

Use function baseline for baseline correction. This function takes matrices of spectra, a method name and parameters needed for the specific method. See helpfiles for details.

References

Andreas F. Ruckstuhl, Matthew P. Jacobson, Robert W. Field, James A. Dodd: Baseline subtraction using robust local regression estimation; CHAD A. LIEBER and ANITA MAHADEVAN-JANSEN: Automated Method for Subtraction of Fluorescence from Biological Raman Spectra; Mark S. Friedrichs: A model-free algorithm for the removal of baseline artifacts; AHMET K. ATAKAN, W. E. BLASS, and D. E. JENNINGS: Elimination of Baseline Variations from a Recorded Spectrum by Ultra-low Frequency Filtering; M.A. Kneen, H.J. Annegarn: Algorithm for fitting XRF, SEM and PIXE X-ray spectra backgrounds; K.H. Liland, B.-H. Mevik, E.-O. Rukke, T. Almøy, M. Skaugen and T. Isaksson (2009) Quantitative whole spectrum analysis with MALDI-TOF MS, Part I: Measurement optimisation. Chemometrics and Intelligent Laboratory Systems, 96(2), 210--218.

Examples

# Load data
data(milk)
# The baseline() function is an S4 wrapper for all the different 
# baseline correction methods. The default correction method
# is IRLS. Data must be organized as row vectors in a matrix
# or data.frame.
bc.irls <- baseline(milk$spectra[1,, drop=FALSE])
if (FALSE) {
  # Computationally heavy
	plot(bc.irls)
}

# Available extractors are:
# getBaseline(bc.irls)
# getSpectra(bc.irls)
# getCorrected(bc.irls)
# getCall(bc.irls)

# Correction methods and parameters can be specified through the wrapper.
bc.fillPeaks <- baseline(milk$spectra[1,, drop=FALSE], lambda=6,
	hwi=50, it=10, int=2000, method='fillPeaks')
if (FALSE) {
  # Computationally heavy
	plot(bc.fillPeaks)
}

# If a suitable gWidgets2 implementation is installed, a 
# graphical user interface is available for interactive
# parameter adaption.
if (FALSE) {
  # Dependent on external software
  baselineGUI(milk$spectra)
}