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.

AuthorKristian Hovde Liland [aut, cre], Bjørn-Helge Mevik [aut], Roberto Canteri [ctb]
Date of publication2015-07-05 23:57:57
MaintainerKristian Hovde Liland <kristian.liland@nmbu.no>
LicenseGPL-2
Version1.2-1

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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