# Baseline Correction of Spectra

## Documentation for package ‘baseline’ version 1.3-1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F G I L M N O P Q R S T

baseline-package | Baseline correction

## -- A --

algorithm | Extraction methods for "baselineAlgTest" objects
algorithm-method | Extraction methods for "baselineAlgTest" objects
algorithm-methods | Extraction methods for "baselineAlgTest" objects
als | Asymmetric Least Squares

## -- B --

baseline | Baseline correction
baseline-class | Class "baseline"
baseline.als | Asymmetric Least Squares
baseline.fillPeaks | Fill peaks
baseline.irls | Iterative Restricted Least Squares
baseline.lowpass | Low-pass FFT filter
baseline.medianWindow | Median window
baseline.modpolyfit | Modified polynomial fitting
baseline.peakDetection | Simultaneous Peak Detection and Baseline Correction
baseline.rfbaseline | Robust Baseline Estimation
baseline.rollingBall | Rolling ball
baseline.shirley | Shirley Background Estimation
baseline.TAP | TAP
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"
baselineEnv | Baseline environment
baselineGUI | Interactive plotting tool

## -- C --

C1s | XPS core line data
custom.baseline | Customized baseline correction

## -- D --

description | Extraction methods for "baselineAlg" objects
description-method | Extraction methods for "baselineAlg" objects
description-methods | Extraction methods for "baselineAlg" objects
doOptim | Optimise several baseline algorithms on a data set

## -- E --

extraArgs | Extraction methods for "baselineAlgTest" objects
extraArgs-method | Extraction methods for "baselineAlgTest" objects
extraArgs-methods | Extraction methods for "baselineAlgTest" objects

## -- F --

fillPeaks | Fill peaks
funcName | Extract the "funcName" slot.
funcName-method | Extract the "funcName" slot.
funcName-methods | Extract the "funcName" slot.

## -- G --

getBaseline | Functions to extract the components of a "baseline" object
getBaseline-method | Class "baseline"
getBaselineEnv | Baseline environment
getCall | Functions to extract the components of a "baseline" object
getCall-method | Class "baseline"
getCorrected | Functions to extract the components of a "baseline" object
getCorrected-method | Class "baseline"
getOptim | Visual tool for setting up optimization
getOptimRes | Visual tool for setting up optimization
getSpectra | Functions to extract the components of a "baseline" object
getSpectra-method | Class "baseline"

## -- I --

ind.min | Extraction methods specific for "predictionResult" objects
ind.min-method | Extraction methods specific for "predictionResult" objects
ind.min-methods | Extraction methods specific for "predictionResult" objects
irls | Iterative Restricted Least Squares

## -- L --

lowpass | Low-pass FFT filter

## -- M --

medianWindow | Median window
milk | MALDI-TOF mass spectra
minQualMeas | Extraction functions for "predictionResult" or "baselineAlgResult" objects
minQualMeas-method | Extraction functions for "predictionResult" or "baselineAlgResult" objects
minQualMeas-methods | Extraction functions for "predictionResult" or "baselineAlgResult" objects
modpolyfit | Modified polynomial fitting
mvrValstats | Optimise several baseline algorithms on a data set

## -- N --

name | Extraction methods for "baselineAlg" objects
name-method | Extraction methods for "baselineAlg" objects
name-methods | Extraction methods for "baselineAlg" objects

## -- O --

O1s | XPS core line data
optimWizard | Visual tool for setting up optimization
overall.min | Extract the minimum from a baseline optimisation

## -- P --

param | Extract the "param" slot
param-method | Extract the "param" slot
param-methods | Extract the "param" slot
param.ind.min | Extraction methods for "baselineAlgResult" objects
param.ind.min-method | Extraction methods for "baselineAlgResult" objects
param.ind.min-methods | Extraction methods for "baselineAlgResult" objects
param.min | Extraction functions for "predictionResult" or "baselineAlgResult" objects
param.min-method | Extraction functions for "predictionResult" or "baselineAlgResult" objects
param.min-methods | Extraction functions for "predictionResult" or "baselineAlgResult" objects
paramName | Extraction methods specific for "predictionResult" objects
paramName-method | Extraction methods specific for "predictionResult" objects
paramName-methods | Extraction methods specific for "predictionResult" objects
peakDetection | Simultaneous Peak Detection and Baseline Correction
plot-method | Plot method for "baseline" 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"
putBaselineEnv | Baseline environment

## -- Q --

qualMeas | Extraction functions for "predictionResult" or "baselineAlgResult" objects
qualMeas-method | Extraction functions for "predictionResult" or "baselineAlgResult" objects
qualMeas-methods | Extraction functions for "predictionResult" or "baselineAlgResult" objects
qualMeas.ind.min | Extraction methods for "baselineAlgResult" objects
qualMeas.ind.min-method | Extraction methods for "baselineAlgResult" objects
qualMeas.ind.min-methods | Extraction methods for "baselineAlgResult" objects
qualMeasName | Extraction functions for "predictionResult" or "baselineAlgResult" objects
qualMeasName-method | Extraction functions for "predictionResult" or "baselineAlgResult" objects
qualMeasName-methods | Extraction functions for "predictionResult" or "baselineAlgResult" objects

## -- R --

rfbaseline | Robust Baseline Estimation
ridgeRegressionTest-class | Class "ridgeRegressionTest"
rollingBall | Rolling ball
runTest | Run a predictionTest or baselineAlgTest
runTest-method | Run a predictionTest or baselineAlgTest
runTest-methods | Run a predictionTest or baselineAlgTest

## -- S --

shirley | Shirley Background Estimation

## -- T --

TAP | TAP