baseline-package {baseline} | R Documentation

## Baseline correction

### Description

A common framework with implementations of several baseline correction methods

### Details

Package: | baseline
Type: | Package
Version: | 1.2-1
Date: | 2015-07-05
License: | GPL-2

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.

### Author(s)

Kristian Hovde Liland and Bjørn-Helge Mevik

Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

### 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])
    ## Not run:
      # Computationally heavy
    	plot(bc.irls)

    ## End(Not run)

    # 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')
    ## Not run:
      # Computationally heavy
    	plot(bc.fillPeaks)

    ## End(Not run)

    # If a suitable gWidgets implementation is installed, a
    # graphical user interface is available for interactive
    # parameter adaption.
    ## Not run:
      # Dependent on external software
      baselineGUI(milk$spectra)

    ## End(Not run)

[Package baseline version 1.2-1 Index]