Package: baseline 1.3-8

baseline: Baseline Correction of Spectra

Collection of baseline correction algorithms, along with a framework and a Tcl/Tk enabled 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.

Authors:Kristian Hovde Liland [aut, cre], Bjørn-Helge Mevik [aut], Roberto Canteri [ctb]

baseline_1.3-8.tar.gz
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baseline_1.3-8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
baseline/json (API)

# Install 'baseline' in R:
install.packages('baseline', repos = c('https://khliland.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/khliland/baseline/issues

Uses libs:
  • openblas– Optimized BLAS
Datasets:
  • C1s - XPS core line data
  • milk - MALDI-TOF mass spectra
  • O1s - XPS core line data

On CRAN:

Conda:

openblas

7.10 score 12 stars 9 packages 88 scripts 1.1k downloads 8 mentions 47 exports 1 dependencies

Last updated from:722bbfe4e6. Checks:14 OK, 1 WARNING. Indexed: yes.

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source / vignettesOK217
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linux-release-x86_64OK152
macos-release-arm64OK124
macos-release-x86_64OK288
macos-oldrel-arm64OK122
macos-oldrel-x86_64OK289
windows-devel-arm64OK208
windows-devel-x86_64OK129
windows-release-arm64WARNING191
windows-release-x86_64OK100
windows-oldrel-x86_64OK113
wasm-releaseOK140

Exports:algorithmbaselinebaseline.alsbaseline.fillPeaksbaseline.irlsbaseline.lowpassbaseline.medianWindowbaseline.modpolyfitbaseline.peakDetectionbaseline.rfbaselinebaseline.rollingBallbaseline.shirleybaseline.TAPbaselineAlgorithmsbaselineAlgorithmsGUIbaselineEnvbaselineGUIcustom.baselinedescriptiondoOptimextraArgsfuncNamegetBaselinegetBaselineEnvgetCallgetCorrectedgetOptimgetOptimResgetSpectraind.minminQualMeasmvrValstatsnameoptimWizardoverall.minparamparam.ind.minparam.minparamNameplotplotBaselineplotOptimputBaselineEnvqualMeasqualMeas.ind.minqualMeasNamerunTest

Dependencies:SparseM

Readme and manuals

Help Manual

Help pageTopics
Baseline correctionbaseline-package
Extraction methods for "baselineAlgTest" objectsalgorithm algorithm,baselineAlgTest-method algorithm-methods extraArgs extraArgs,baselineAlgTest-method extraArgs-methods
Baseline correctionbaseline
Asymmetric Least Squaresals baseline.als
Fill peaksbaseline.fillPeaks fillPeaks
Iterative Restricted Least Squaresbaseline.irls irls
Low-pass FFT filterbaseline.lowpass lowpass
Median windowbaseline.medianWindow medianWindow
Modified polynomial fittingbaseline.modpolyfit modpolyfit
Simultaneous Peak Detection and Baseline Correctionbaseline.peakDetection peakDetection
Robust Baseline Estimationbaseline.rfbaseline rfbaseline
Rolling ballbaseline.rollingBall rollingBall
Shirley Background Estimationbaseline.shirley shirley
TAPbaseline.TAP TAP
Extraction methods for "baselineAlg" objectsbaselineAlg description description,baselineAlg-method description-methods name name,baselineAlg-method name-methods
Class "baselineAlg"baselineAlg-class baselineAlgClass
List of available baseline algorithmsbaselineAlgorithms
List of available baseline algorithms for GUI functionbaselineAlgorithmsGUI
Class "baselineAlgResult"baselineAlgResult baselineAlgResult-class
Extraction methods for "baselineAlgResult" objectsbaselineAlgResultMethods param.ind.min param.ind.min,baselineAlgResult-method param.ind.min-methods qualMeas.ind.min qualMeas.ind.min,baselineAlgResult-method qualMeas.ind.min-methods
Class "baselineAlgTest"baselineAlgTest baselineAlgTest-class
Class "baseline"baseline-class baselineClass
Baseline environmentbaselineEnv getBaselineEnv putBaselineEnv
Interactive plotting toolbaselineGUI
Customized baseline correctioncustom.baseline
Optimise several baseline algorithms on a data setdoOptim mvrValstats
Extract the "funcName" slot.funcName funcName,baselineAlg-method funcName,baselineAlgTest-method funcName-methods
Functions to extract the components of a "baseline" objectgetBaseline getBaseline,baseline-method getCall getCall,baseline-method getCorrected getCorrected,baseline-method getSpectra getSpectra,baseline-method
MALDI-TOF mass spectramilk
Visual tool for setting up optimizationgetOptim getOptimRes optimWizard
Extract the minimum from a baseline optimisationoverall.min
Extract the "param" slotparam param,baselineAlg-method param,baselineAlgResult-method param,baselineAlgTest-method param,predictionResult-method param-methods
Plot method for "baseline" objectsplot,baseline-method plotBaseline
Plotting tool for result objects from optimizationplotOptim
Class "PLSRTest"PLSRTest-class PLSRTestClass
Class "predictionResult"predictionResult predictionResult-class
Extraction methods specific for "predictionResult" objectsind.min ind.min,predictionResult-method ind.min-methods paramName paramName,predictionResult-method paramName-methods predictionResultMethods
Class "predictionTest"predictionTest predictionTest-class predictionTestClass
Extraction functions for "predictionResult" or "baselineAlgResult" objects.minQualMeas minQualMeas,baselineAlgResult-method minQualMeas,predictionResult-method minQualMeas-methods param.min param.min,baselineAlgResult-method param.min,predictionResult-method param.min-methods qualMeas qualMeas,baselineAlgResult-method qualMeas,predictionResult-method qualMeas-methods qualMeasName qualMeasName,baselineAlgResult-method qualMeasName,predictionResult-method qualMeasName-methods
Class "ridgeRegressionTest"ridgeRegressionTest-class ridgeRegressionTestClass
Run a predictionTest or baselineAlgTestrunTest runTest,baselineAlgTest-method runTest,PLSRTest-method runTest,ridgeRegressionTest-method runTest-methods
XPS core line dataC1s O1s XPSdata