Package: baseline 1.3-5
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:
baseline_1.3-5.tar.gz
baseline_1.3-5.zip(r-4.5)baseline_1.3-5.zip(r-4.4)baseline_1.3-5.zip(r-4.3)
baseline_1.3-5.tgz(r-4.4-any)baseline_1.3-5.tgz(r-4.3-any)
baseline_1.3-5.tar.gz(r-4.5-noble)baseline_1.3-5.tar.gz(r-4.4-noble)
baseline_1.3-5.tgz(r-4.4-emscripten)baseline_1.3-5.tgz(r-4.3-emscripten)
baseline.pdf |baseline.html✨
baseline/json (API)
NEWS
| # 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
Last updated 4 months agofrom:4637f6a35f. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 24 2024 |
| R-4.5-win | OK | Aug 24 2024 |
| R-4.5-linux | OK | Aug 24 2024 |
| R-4.4-win | OK | Aug 24 2024 |
| R-4.4-mac | OK | Aug 24 2024 |
| R-4.3-win | OK | Aug 24 2024 |
| R-4.3-mac | OK | Aug 24 2024 |
Exports:algorithmbaselinebaseline.alsbaseline.fillPeaksbaseline.irlsbaseline.lowpassbaseline.medianWindowbaseline.modpolyfitbaseline.peakDetectionbaseline.rfbaselinebaseline.rollingBallbaseline.shirleybaseline.TAPbaselineAlgorithmsbaselineAlgorithmsGUIbaselineEnvbaselineGUIcustom.baselinedescriptiondoOptimextraArgsfuncNamegetBaselinegetBaselineEnvgetCallgetCorrectedgetOptimgetOptimResgetSpectraind.minminQualMeasmvrValstatsnameoptimWizardoverall.minparamparam.ind.minparam.minparamNameplotplotBaselineplotOptimputBaselineEnvqualMeasqualMeas.ind.minqualMeasNamerunTest
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Baseline correction | baseline-package |
| Extraction methods for "baselineAlgTest" objects | algorithm algorithm,baselineAlgTest-method algorithm-methods extraArgs extraArgs,baselineAlgTest-method extraArgs-methods |
| Baseline correction | baseline |
| Class "baseline" | baseline-class getBaseline,baseline-method getCall,baseline-method getCorrected,baseline-method getSpectra,baseline-method |
| Asymmetric Least Squares | als baseline.als |
| Fill peaks | baseline.fillPeaks fillPeaks |
| Iterative Restricted Least Squares | baseline.irls irls |
| Low-pass FFT filter | baseline.lowpass lowpass |
| Median window | baseline.medianWindow medianWindow |
| Modified polynomial fitting | baseline.modpolyfit modpolyfit |
| Simultaneous Peak Detection and Baseline Correction | baseline.peakDetection peakDetection |
| Robust Baseline Estimation | baseline.rfbaseline rfbaseline |
| Rolling ball | baseline.rollingBall rollingBall |
| Shirley Background Estimation | baseline.shirley shirley |
| TAP | baseline.TAP TAP |
| Class "baselineAlg" | baselineAlg-class |
| List of available baseline algorithms | baselineAlgorithms |
| List of available baseline algorithms for GUI function | baselineAlgorithmsGUI |
| Class "baselineAlgResult" | baselineAlgResult-class |
| Class "baselineAlgTest" | baselineAlgTest-class |
| Baseline environment | baselineEnv getBaselineEnv putBaselineEnv |
| Interactive plotting tool | baselineGUI |
| Customized baseline correction | custom.baseline |
| Optimise several baseline algorithms on a data set | doOptim mvrValstats |
| Extract the "funcName" slot. | funcName funcName,baselineAlg-method funcName,baselineAlgTest-method funcName-methods |
| Functions to extract the components of a "baseline" object | getBaseline getCall getCorrected getSpectra |
| Extraction methods specific for "predictionResult" objects | ind.min ind.min,predictionResult-method ind.min-methods paramName paramName,predictionResult-method paramName-methods |
| MALDI-TOF mass spectra | milk |
| Extraction methods for "baselineAlg" objects | description description,baselineAlg-method description-methods name name,baselineAlg-method name-methods |
| Visual tool for setting up optimization | getOptim getOptimRes optimWizard |
| Extract the minimum from a baseline optimisation | overall.min |
| Extract the "param" slot | param param,baselineAlg-method param,baselineAlgResult-method param,baselineAlgTest-method param,predictionResult-method param-methods |
| Extraction methods for "baselineAlgResult" objects | param.ind.min param.ind.min,baselineAlgResult-method param.ind.min-methods qualMeas.ind.min qualMeas.ind.min,baselineAlgResult-method qualMeas.ind.min-methods |
| Plot method for "baseline" objects | plot,baseline-method plotBaseline |
| Plotting tool for result objects from optimization | plotOptim |
| Class "PLSRTest" | PLSRTest-class |
| Class "predictionResult" | predictionResult-class |
| Class "predictionTest" | predictionTest-class |
| 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 |
| Run a predictionTest or baselineAlgTest | runTest runTest,baselineAlgTest-method runTest,PLSRTest-method runTest,ridgeRegressionTest-method runTest-methods |
| XPS core line data | C1s O1s |
