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.

Install the latest version of this package by entering the following in R:
install.packages("baseline")
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

Functions

algorithm Man page
algorithm,baselineAlgTest-method Man page
algorithm-methods Man page
baseline Man page
baselineAlg-class Man page
baselineAlgorithms Man page
baselineAlgorithmsGUI Man page
baselineAlgResult-class Man page
baselineAlgTest-class Man page
baseline.als Man page
baseline-class Man page
baselineEnv Man page
baseline.fillPeaks Man page
baselineGUI Man page
baseline.irls Man page
baseline.lowpass Man page
baseline.medianWindow Man page
baseline.modpolyfit Man page
baseline-package Man page
baseline.peakDetection Man page
baseline.rfbaseline Man page
baseline.rollingBall Man page
baseline.shirley Man page
C1s Man page
custom.baseline Man page
description Man page
description,baselineAlg-method Man page
description-methods Man page
doOptim Man page
extraArgs Man page
extraArgs,baselineAlgTest-method Man page
extraArgs-methods Man page
funcName Man page
funcName,baselineAlg-method Man page
funcName,baselineAlgTest-method Man page
funcName-methods Man page
getBaseline Man page
getBaseline,baseline-method Man page
getBaselineEnv Man page
getCall Man page
getCall,baseline-method Man page
getCorrected Man page
getCorrected,baseline-method Man page
getOptim Man page
getOptimRes Man page
getSpectra Man page
getSpectra,baseline-method Man page
ind.min Man page
ind.min-methods Man page
ind.min,predictionResult-method Man page
milk Man page
minQualMeas Man page
minQualMeas,baselineAlgResult-method Man page
minQualMeas-methods Man page
minQualMeas,predictionResult-method Man page
mvrValstats Man page
name Man page
name,baselineAlg-method Man page
name-methods Man page
O1s Man page
optimWizard Man page
overall.min Man page
param Man page
param,baselineAlg-method Man page
param,baselineAlgResult-method Man page
param,baselineAlgTest-method Man page
param.ind.min Man page
param.ind.min,baselineAlgResult-method Man page
param.ind.min-methods Man page
param-methods Man page
param.min Man page
param.min,baselineAlgResult-method Man page
param.min-methods Man page
param.min,predictionResult-method Man page
paramName Man page
paramName-methods Man page
paramName,predictionResult-method Man page
param,predictionResult-method Man page
plotBaseline Man page
plot,baseline-method Man page
plotOptim Man page
PLSRTest-class Man page
predictionResult-class Man page
predictionTest-class Man page
putBaselineEnv Man page
qualMeas Man page
qualMeas,baselineAlgResult-method Man page
qualMeas.ind.min Man page
qualMeas.ind.min,baselineAlgResult-method Man page
qualMeas.ind.min-methods Man page
qualMeas-methods Man page
qualMeasName Man page
qualMeasName,baselineAlgResult-method Man page
qualMeasName-methods Man page
qualMeasName,predictionResult-method Man page
qualMeas,predictionResult-method Man page
ridgeRegressionTest-class Man page
runTest Man page
runTest,baselineAlgTest-method Man page
runTest-methods Man page
runTest,PLSRTest-method Man page
runTest,ridgeRegressionTest-method Man page

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.