baseline: Baseline Correction of Spectra

Collection of baseline correction algorithms, along with a framework and a GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.

Author
Kristian Hovde Liland [aut, cre], Bjørn-Helge Mevik [aut], Roberto Canteri [ctb]
Date of publication
2015-07-05 23:57:57
Maintainer
Kristian Hovde Liland <kristian.liland@nmbu.no>
License
GPL-2
Version
1.2-1

View on CRAN

Man pages

algorithm
Extraction methods for "baselineAlgTest" objects
baseline
Baseline correction
baselineAlg-class
Class "baselineAlg"
baselineAlgorithms
List of available baseline algorithms
baselineAlgorithmsGUI
List of available baseline algorithms for GUI function
baselineAlgResult-class
Class "baselineAlgResult"
baselineAlgTest-class
Class "baselineAlgTest"
baseline.als
Asymmetric Least Squares
baseline-class
Class "baseline"
baselineEnv
Baseline environment
baseline.fillPeaks
Fill peaks
baselineGUI
Interactive plotting tool
baseline.irls
Iterative Restricted Least Squares
baseline.lowpass
Low-pass FFT filter
baseline.medianWindow
Median window
baseline.modpolyfit
Modified polynomial fitting
baseline-package
Baseline correction
baseline.peakDetection
Simultaneous Peak Detection and Baseline Correction
baseline.rfbaseline
Robust Baseline Estimation
baseline.rollingBall
Rolling ball
baseline.shirley
Shirley Background Estimation
custom.baseline
Customized baseline correction
doOptim
Optimise several baseline algorithms on a data set
funcName
Extract the "funcName" slot.
getBaseline
Functions to extract the components of a "baseline" object
ind.min
Extraction methods specific for "predictionResult" objects
milk
MALDI-TOF mass spectra
name
Extraction methods for "baselineAlg" objects
optimWizard
Visual tool for setting up optimization
overall.min
Extract the minimum from a baseline optimisation
param
Extract the "param" slot
param.ind.min
Extraction methods for "baselineAlgResult" objects
plotBaseline
Plot method for "baseline" objects
plotOptim
Plotting tool for result objects from optimization
PLSRTest-class
Class "PLSRTest"
predictionResult-class
Class "predictionResult"
predictionTest-class
Class "predictionTest"
qualMeas
Extraction functions for "predictionResult" or...
ridgeRegressionTest-class
Class "ridgeRegressionTest"
runTest
Run a predictionTest or baselineAlgTest
XPSdata
XPS core line data

Files in this package

baseline
baseline/NAMESPACE
baseline/NEWS
baseline/data
baseline/data/milk.rda
baseline/data/C1s.RData
baseline/data/O1s.rda
baseline/data/datalist
baseline/R
baseline/R/baseline.rollingBall.R
baseline/R/baseline.modpolyfit.R
baseline/R/aaa.R
baseline/R/baseline.rfbaseline.R
baseline/R/baselineGUI.R
baseline/R/baseline.fillPeaks.R
baseline/R/custom.baseline.R
baseline/R/baseline.peakDetection.R
baseline/R/baseline.irls.R
baseline/R/baseline.shirley.R
baseline/R/globals.R
baseline/R/baseline.als.R
baseline/R/plotBaseline.R
baseline/R/optimisation.R
baseline/R/plotOptim.R
baseline/R/optimWizard.R
baseline/R/baseline.medianWindow.R
baseline/R/baseline.lowpass.R
baseline/R/baseline.R
baseline/MD5
baseline/DESCRIPTION
baseline/man
baseline/man/baselineGUI.Rd
baseline/man/custom.baseline.Rd
baseline/man/baselineAlgTest-class.Rd
baseline/man/funcName.Rd
baseline/man/optimWizard.Rd
baseline/man/baseline-class.Rd
baseline/man/plotOptim.Rd
baseline/man/baseline.modpolyfit.Rd
baseline/man/param.Rd
baseline/man/milk.Rd
baseline/man/baseline.Rd
baseline/man/baseline.fillPeaks.Rd
baseline/man/plotBaseline.Rd
baseline/man/XPSdata.Rd
baseline/man/qualMeas.Rd
baseline/man/baselineAlgorithms.Rd
baseline/man/ridgeRegressionTest-class.Rd
baseline/man/baselineAlg-class.Rd
baseline/man/getBaseline.Rd
baseline/man/baseline.rfbaseline.Rd
baseline/man/baseline.irls.Rd
baseline/man/ind.min.Rd
baseline/man/doOptim.Rd
baseline/man/runTest.Rd
baseline/man/name.Rd
baseline/man/baseline-package.Rd
baseline/man/overall.min.Rd
baseline/man/predictionResult-class.Rd
baseline/man/baselineAlgResult-class.Rd
baseline/man/baseline.als.Rd
baseline/man/baseline.rollingBall.Rd
baseline/man/baselineEnv.Rd
baseline/man/baseline.lowpass.Rd
baseline/man/baseline.peakDetection.Rd
baseline/man/param.ind.min.Rd
baseline/man/baselineAlgorithmsGUI.Rd
baseline/man/PLSRTest-class.Rd
baseline/man/baseline.shirley.Rd
baseline/man/predictionTest-class.Rd
baseline/man/algorithm.Rd
baseline/man/baseline.medianWindow.Rd