mdatools: Multivariate Data Analysis for Chemometrics

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Package implements projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics.

Author
Sergey Kucheryavskiy
Date of publication
2015-11-30 21:23:13
Maintainer
Sergey Kucheryavskiy <svkucheryavski@gmail.com>
License
GPL-3
Version
0.7.0

View on CRAN

Man pages

as.matrix.classres
as.matrix method for classification results
as.matrix.ldecomp
as.matrix method for ldecomp object
as.matrix.plsdares
as.matrix method for PLS-DA results
as.matrix.plsres
as.matrix method for PLS results
as.matrix.regcoeffs
as.matrix method for regression coefficients class
as.matrix.regres
as.matrix method for regression results
bars
Show bars on axes
classify.plsda
PLS-DA classification
classres
Results of classification
crossval
Generate sequence of indices for cross-validation
crossval.str
String with description of cross-validation method
erfinv
Inverse error function
errorbars
Show error bars on a plot
getCalibrationData
Calibration data
getCalibrationData.pca
Get calibration data
getCalibrationData.simcam
Get calibration data
getClassificationPerformance
Calculation of classification performance parameters
getMainTitle
Get main title
getRegcoeffs
Get regression coefficients
getRegcoeffs.pls
Regression coefficients for PLS model'
getSelectedComponents
Get selected components
getSelectedComponents.classres
Get selected components
getSelectivityRatio
Selectivity ratio
getSelectivityRatio.pls
Selectivity ratio for PLS model
getVIPScores
VIP scores
getVIPScores.pls
VIP scores for PLS model
ipls
Variable selection with interval PLS
ipls.backward
Runs the backward iPLS algorithm
ipls.forward
Runs the forward iPLS algorithm
ldecomp
Linear decomposition of data
ldecomp.getDistances
Residuals distances for linear decomposition
ldecomp.getResLimits
Statistical limits for Q and T2 residuals
ldecomp.getVariances
Explained variance for linear decomposition
mdaplot
Plotting function for a single set of objects
mdaplot.areColors
Check color values
mdaplot.formatValues
Format vector with numeric values
mdaplotg
Plotting function for several sets of objects
mdaplot.getAxesLim
Calculate axes limits
mdaplot.getColors
Color values for plot elements
mdaplot.plotAxes
Create axes plane
mdaplot.showColorbar
Plot colorbar
mdaplot.showGrid
Plot grid
mdaplot.showLabels
Plot labels Shows labels for data elements (points, bars) on...
mdaplot.showLegend
Plot legend
mdaplot.showLines
Plot lines
mdaplot.showRegressionLine
Regression line for data points
mdatools
Package for Multivariate Data Analysis (Chemometrics)
pca
Principal Component Analysis
pca.cal
PCA model calibration
pca.crossval
Cross-validation of a PCA model
pca.mvreplace
Replace missing values in data
pca.nipals
NIPALS based PCA algorithm
pcares
Results of PCA decomposition
pca.svd
Singular Values Decomposition based PCA algorithm
People
People data
pinv
Pseudo-inverse matrix
plot.classres
Plot function for classification results
plotCooman
Cooman's plot
plotCooman.simcam
Cooman's plot for SIMCAM model
plotCooman.simcamres
Cooman's plot for SIMCAM results
plotCorr
Correlation plot
plotCorr.randtest
Correlation plot for randomization test results
plotCumVariance
Variance plot
plotCumVariance.ldecomp
Cumulative explained variance plot for linear decomposition
plotCumVariance.pca
Cumulative explained variance plot for PCA
plotDiscriminationPower
Discrimination power plot
plotDiscriminationPower.simcam
Discrimination power plot for SIMCAM model
plotHist
Statistic histogram
plotHist.randtest
Histogram plot for randomization test results
plot.ipls
Overview plot for iPLS results
plotLoadings
Loadings plot
plotLoadings.pca
Loadings plot for PCA
plotMisclassified
Misclassification ratio plot
plotMisclassified.classmodel
Misclassified ratio plot for classification model
plotMisclassified.classres
Misclassified ratio plot for classification results
plotModelDistance
Model distance plot
plotModelDistance.simcam
Modelling distance plot for SIMCAM model
plotModellingPower
Modelling power plot
plotModellingPower.simca
Modelling power plot for SIMCA model
plotModellingPower.simcam
Modelling power plot for SIMCAM model
plot.pca
Model overview plot for PCA
plot.pcares
Plot method for PCA results object
plotPerformance
Classification performance plot
plotPerformance.classmodel
Performance plot for classification model
plotPerformance.classres
Performance plot for classification results
plot.pls
Model overview plot for PLS
plot.plsda
Model overview plot for PLS-DA
plot.plsdares
Overview plot for PLS-DA results
plot.plsres
Overview plot for PLS results
plotPredictions
Predictions plot
plotPredictions.classmodel
Predictions plot for classification model
plotPredictions.classres
Prediction plot for classification results
plotPredictions.pls
Predictions plot for PLS
plotPredictions.plsres
Predictions plot for PLS results
plotPredictions.regres
Predictions plot for regression results
plot.randtest
Plot for randomization test results
plot.regcoeffs
Regression coefficients plot
plotRegcoeffs
Regression coefficients plot
plotRegcoeffs.pls
Regression coefficient plot for PLS
plot.regres
plot method for regression results
plotResiduals
Residuals plot
plotResiduals.ldecomp
Residuals plot for linear decomposition
plotResiduals.pca
Residuals plot for PCA
plotResiduals.simcam
Residuals plot for SIMCAM model
plotResiduals.simcamres
Residuals plot for SIMCAM results
plotResiduals.simcares
Residuals plot for SIMCA results
plotRMSE
RMSE plot
plotRMSE.ipls
RMSE development plot
plotRMSE.pls
RMSE plot for PLS
plotRMSE.plsres
RMSE plot for PLS results
plotRMSE.regres
RMSE plot for regression results
plotScores
Scores plot
plotScores.ldecomp
Scores plot for linear decomposition
plotScores.pca
Scores plot for PCA
plotSelection
Selected intervals plot
plotSelection.ipls
iPLS performance plot
plotSelectivityRatio
Selectivity ratio plot
plotSelectivityRatio.pls
Selectivity ratio plot for PLS model
plotSensitivity
Sensitivity plot
plotSensitivity.classmodel
Sensitivity plot for classification model
plotSensitivity.classres
Sensitivity plot for classification results
plot.simca
Model overview plot for SIMCA
plot.simcam
Model overview plot for SIMCAM
plot.simcamres
Model overview plot for SIMCAM results
plotSpecificity
Specificity plot
plotSpecificity.classmodel
Specificity plot for classification model
plotSpecificity.classres
Specificity plot for classification results
plotVariance
Variance plot
plotVariance.ldecomp
Explained variance plot for linear decomposition
plotVariance.pca
Explained variance plot for PCA
plotVariance.pls
Variance plot for PLS
plotVIPScores
VIP scores plot
plotVIPScores.pls
VIP scores plot for PLS model
plotXCumVariance
X cumulative variance plot
plotXCumVariance.pls
Cumulative explained X variance plot for PLS
plotXCumVariance.plsres
Explained cumulative X variance plot for PLS results
plotXLoadings
X loadings plot
plotXLoadings.pls
X loadings plot for PLS
plotXResiduals
X residuals plot
plotXResiduals.pls
X residuals plot for PLS
plotXResiduals.plsres
X residuals plot for PLS results
plotXScores
X scores plot
plotXScores.pls
X scores plot for PLS
plotXScores.plsres
X scores plot for PLS results
plotXVariance
X variance plot
plotXVariance.pls
Explained X variance plot for PLS
plotXVariance.plsres
Explained X variance plot for PLS results
plotXYLoadings
X loadings plot
plotXYLoadings.pls
XY loadings plot for PLS
plotXYScores
XY scores plot
plotXYScores.pls
XY scores plot for PLS
plotXYScores.plsres
XY scores plot for PLS results
plotYCumVariance
Y cumulative variance plot
plotYCumVariance.pls
Cumulative explained Y variance plot for PLS
plotYCumVariance.plsres
Explained cumulative Y variance plot for PLS results
plotYResiduals
Y residuals plot
plotYResiduals.pls
Y residuals plot for PLS
plotYResiduals.regres
Residuals plot for regression results
plotYVariance
Y variance plot
plotYVariance.pls
Explained Y variance plot for PLS
plotYVariance.plsres
Explained Y variance plot for PLS results
pls
Partial Least Squares regression
pls.cal
PLS model calibration
pls.calculateSelectivityRatio
Selectivity ratio calculation
pls.calculateVIPScores
VIP scores calculation for PLS model
pls.crossval
Cross-validation of a PLS model
plsda
Partial Least Squares Discriminant Analysis
plsda.crossval
Cross-validation of a PLS-DA model
plsda.getReferenceValues
Reference values for PLS-DA
plsdares
PLS-DA results
plsres
PLS results
pls.simpls
SIMPLS algorithm
predict.pca
PCA predictions
predict.pls
PLS predictions
predict.plsda
PLS-DA predictions
predict.simca
SIMCA predictions
predict.simcam
SIMCA multiple classes predictions
prep.autoscale
Autoscale values
prep.msc
Multiplicative Scatter Correction transformation
prep.norm
Normalization
prep.savgol
Savytzky-Golay filter
prep.snv
Standard Normal Variate transformation
print.classres
Print information about classification result object
print.ipls
Print method for iPLS
print.ldecomp
Print method for linear decomposition
print.pca
Print method for PCA model object
print.pcares
Print method for PCA results object
print.pls
Print method for PLS model object
print.plsda
Print method for PLS-DA model object
print.plsdares
Print method for PLS-DA results object
print.plsres
print method for PLS results object
print.randtest
Print method for randtest object
print.regcoeffs
print method for regression coefficients class
print.regres
print method for regression results object
print.simca
Print method for SIMCA model object
print.simcam
Print method for SIMCAM model object
print.simcamres
Print method for SIMCAM results object
print.simcares
Print method for SIMCA results object
randtest
Randomization test for PLS regression
regcoeffs
Regression coefficients
regcoeffs.getStat
Confidence intervals and p-values for regression...
regres
Regression results
regres.bias
Prediction bias
regres.r2
Determination coefficient
regres.rmse
RMSE
regres.slope
Slope
selectCompNum
Select optimal number of components for a model
selectCompNum.pca
Select optimal number of components for PCA model
selectCompNum.pls
Select optimal number of components for PLS model
showPredictions
Predictions
showPredictions.classres
Show predicted class values
simca
SIMCA one-class classification
simca.classify
SIMCA classification
simca.crossval
Cross-validation of a SIMCA model
simcam
SIMCA multiclass classification
simcam.getPerformanceStatistics
Performance statistics for SIMCAM model
simcamres
Results of SIMCA multiclass classification
simcares
Results of SIMCA one-class classification
Simdata
Spectral data of polyaromatic hydrocarbons mixing
summary.classres
Summary statistics about classification result object
summary.ipls
Summary for iPLS results
summary.ldecomp
Summary statistics for linear decomposition
summary.pca
Summary method for PCA model object
summary.pcares
Summary method for PCA results object
summary.pls
Summary method for PLS model object
summary.plsda
Summary method for PLS-DA model object
summary.plsdares
Summary method for PLS-DA results object
summary.plsres
summary method for PLS results object
summary.randtest
Summary method for randtest object
summary.regres
summary method for regression results object
summary.simca
Summary method for SIMCA model object
summary.simcam
Summary method for SIMCAM model object
summary.simcamres
Summary method for SIMCAM results object
summary.simcares
Summary method for SIMCA results object

Files in this package

mdatools
mdatools/NAMESPACE
mdatools/NEWS
mdatools/data
mdatools/data/simdata.RData
mdatools/data/people.RData
mdatools/R
mdatools/R/crossval.R
mdatools/R/defaults.R
mdatools/R/pcares.R
mdatools/R/pca.R
mdatools/R/pls.R
mdatools/R/simcares.R
mdatools/R/simcamres.R
mdatools/R/prep.R
mdatools/R/classres.R
mdatools/R/ldecomp.R
mdatools/R/simcam.R
mdatools/R/plsda.R
mdatools/R/ipls.R
mdatools/R/simca.R
mdatools/R/regcoeffs.R
mdatools/R/plsres.R
mdatools/R/regres.R
mdatools/R/mdaplots.R
mdatools/R/randtest.R
mdatools/R/plsdares.R
mdatools/R/misc.R
mdatools/R/classmodel.R
mdatools/README.md
mdatools/MD5
mdatools/DESCRIPTION
mdatools/man
mdatools/man/mdaplot.showRegressionLine.Rd
mdatools/man/regcoeffs.getStat.Rd
mdatools/man/plotSensitivity.Rd
mdatools/man/plotXResiduals.plsres.Rd
mdatools/man/getCalibrationData.pca.Rd
mdatools/man/plotVariance.ldecomp.Rd
mdatools/man/summary.simcam.Rd
mdatools/man/as.matrix.plsdares.Rd
mdatools/man/as.matrix.regcoeffs.Rd
mdatools/man/predict.pca.Rd
mdatools/man/plotSelectivityRatio.Rd
mdatools/man/plotYCumVariance.Rd
mdatools/man/plotResiduals.simcamres.Rd
mdatools/man/print.randtest.Rd
mdatools/man/plotCumVariance.Rd
mdatools/man/print.pls.Rd
mdatools/man/plotResiduals.Rd
mdatools/man/plotYResiduals.pls.Rd
mdatools/man/mdaplot.plotAxes.Rd
mdatools/man/simca.Rd
mdatools/man/summary.plsres.Rd
mdatools/man/summary.simcamres.Rd
mdatools/man/prep.autoscale.Rd
mdatools/man/Simdata.Rd
mdatools/man/mdaplot.showLabels.Rd
mdatools/man/plotModelDistance.Rd
mdatools/man/pls.calculateSelectivityRatio.Rd
mdatools/man/plotDiscriminationPower.Rd
mdatools/man/print.ipls.Rd
mdatools/man/plsda.Rd
mdatools/man/plotXYScores.pls.Rd
mdatools/man/plotLoadings.Rd
mdatools/man/getSelectivityRatio.Rd
mdatools/man/plotCorr.Rd
mdatools/man/getRegcoeffs.pls.Rd
mdatools/man/plotScores.ldecomp.Rd
mdatools/man/regres.r2.Rd
mdatools/man/ipls.backward.Rd
mdatools/man/simcam.Rd
mdatools/man/mdaplot.showColorbar.Rd
mdatools/man/ipls.Rd
mdatools/man/plotSensitivity.classres.Rd
mdatools/man/mdaplot.areColors.Rd
mdatools/man/predict.pls.Rd
mdatools/man/plotModellingPower.simca.Rd
mdatools/man/ldecomp.Rd
mdatools/man/plsdares.Rd
mdatools/man/plotScores.pca.Rd
mdatools/man/pca.cal.Rd
mdatools/man/plot.pcares.Rd
mdatools/man/plot.plsdares.Rd
mdatools/man/mdaplot.getAxesLim.Rd
mdatools/man/summary.plsda.Rd
mdatools/man/plotPredictions.classmodel.Rd
mdatools/man/pls.Rd
mdatools/man/plotModellingPower.Rd
mdatools/man/plotSpecificity.classmodel.Rd
mdatools/man/plotXYScores.Rd
mdatools/man/summary.classres.Rd
mdatools/man/plotYVariance.plsres.Rd
mdatools/man/simcamres.Rd
mdatools/man/ldecomp.getVariances.Rd
mdatools/man/plot.regres.Rd
mdatools/man/mdaplot.showGrid.Rd
mdatools/man/mdaplot.showLegend.Rd
mdatools/man/getCalibrationData.Rd
mdatools/man/regcoeffs.Rd
mdatools/man/plotSelectivityRatio.pls.Rd
mdatools/man/plotYVariance.Rd
mdatools/man/plotLoadings.pca.Rd
mdatools/man/regres.bias.Rd
mdatools/man/plotRMSE.regres.Rd
mdatools/man/showPredictions.Rd
mdatools/man/plotMisclassified.classmodel.Rd
mdatools/man/showPredictions.classres.Rd
mdatools/man/ipls.forward.Rd
mdatools/man/print.simcam.Rd
mdatools/man/predict.simca.Rd
mdatools/man/mdaplot.Rd
mdatools/man/print.ldecomp.Rd
mdatools/man/pcares.Rd
mdatools/man/plotXVariance.pls.Rd
mdatools/man/plot.simcamres.Rd
mdatools/man/plot.simca.Rd
mdatools/man/plsres.Rd
mdatools/man/plotXLoadings.Rd
mdatools/man/plotXScores.pls.Rd
mdatools/man/plot.randtest.Rd
mdatools/man/plotPredictions.plsres.Rd
mdatools/man/print.regres.Rd
mdatools/man/mdaplot.showLines.Rd
mdatools/man/plotRMSE.ipls.Rd
mdatools/man/pls.crossval.Rd
mdatools/man/errorbars.Rd
mdatools/man/plot.ipls.Rd
mdatools/man/pinv.Rd
mdatools/man/plotXVariance.Rd
mdatools/man/plotMisclassified.classres.Rd
mdatools/man/plotXCumVariance.plsres.Rd
mdatools/man/plotXResiduals.pls.Rd
mdatools/man/plotYVariance.pls.Rd
mdatools/man/plotResiduals.simcares.Rd
mdatools/man/crossval.str.Rd
mdatools/man/prep.savgol.Rd
mdatools/man/plotXScores.Rd
mdatools/man/plotModelDistance.simcam.Rd
mdatools/man/simca.classify.Rd
mdatools/man/plotYResiduals.Rd
mdatools/man/plotDiscriminationPower.simcam.Rd
mdatools/man/print.regcoeffs.Rd
mdatools/man/plotYCumVariance.plsres.Rd
mdatools/man/plotSensitivity.classmodel.Rd
mdatools/man/plotCooman.simcamres.Rd
mdatools/man/pca.svd.Rd
mdatools/man/pca.crossval.Rd
mdatools/man/getSelectedComponents.classres.Rd
mdatools/man/print.simcamres.Rd
mdatools/man/plotPredictions.Rd
mdatools/man/plot.plsda.Rd
mdatools/man/pls.calculateVIPScores.Rd
mdatools/man/mdaplot.getColors.Rd
mdatools/man/regres.slope.Rd
mdatools/man/plotXResiduals.Rd
mdatools/man/pls.simpls.Rd
mdatools/man/summary.pls.Rd
mdatools/man/print.pcares.Rd
mdatools/man/simcares.Rd
mdatools/man/classres.Rd
mdatools/man/selectCompNum.pls.Rd
mdatools/man/randtest.Rd
mdatools/man/summary.simcares.Rd
mdatools/man/plotYResiduals.regres.Rd
mdatools/man/plotSelection.Rd
mdatools/man/plotSpecificity.Rd
mdatools/man/plotResiduals.ldecomp.Rd
mdatools/man/plotYCumVariance.pls.Rd
mdatools/man/plotXLoadings.pls.Rd
mdatools/man/regres.rmse.Rd
mdatools/man/as.matrix.ldecomp.Rd
mdatools/man/simcam.getPerformanceStatistics.Rd
mdatools/man/getSelectivityRatio.pls.Rd
mdatools/man/mdaplot.formatValues.Rd
mdatools/man/plotVariance.pca.Rd
mdatools/man/summary.simca.Rd
mdatools/man/getMainTitle.Rd
mdatools/man/predict.simcam.Rd
mdatools/man/plsda.getReferenceValues.Rd
mdatools/man/plotPerformance.Rd
mdatools/man/plotXVariance.plsres.Rd
mdatools/man/bars.Rd
mdatools/man/plotRMSE.plsres.Rd
mdatools/man/plotVIPScores.pls.Rd
mdatools/man/plotPerformance.classres.Rd
mdatools/man/summary.ipls.Rd
mdatools/man/plot.regcoeffs.Rd
mdatools/man/as.matrix.classres.Rd
mdatools/man/plot.plsres.Rd
mdatools/man/plotCorr.randtest.Rd
mdatools/man/plotHist.randtest.Rd
mdatools/man/plotMisclassified.Rd
mdatools/man/print.plsres.Rd
mdatools/man/summary.ldecomp.Rd
mdatools/man/simca.crossval.Rd
mdatools/man/plotSelection.ipls.Rd
mdatools/man/mdaplotg.Rd
mdatools/man/getRegcoeffs.Rd
mdatools/man/pca.Rd
mdatools/man/plotPredictions.classres.Rd
mdatools/man/plot.simcam.Rd
mdatools/man/as.matrix.plsres.Rd
mdatools/man/plotVIPScores.Rd
mdatools/man/getClassificationPerformance.Rd
mdatools/man/plotCumVariance.ldecomp.Rd
mdatools/man/plsda.crossval.Rd
mdatools/man/summary.randtest.Rd
mdatools/man/plotRegcoeffs.Rd
mdatools/man/summary.pcares.Rd
mdatools/man/mdatools.Rd
mdatools/man/getSelectedComponents.Rd
mdatools/man/plotXCumVariance.Rd
mdatools/man/plotCooman.Rd
mdatools/man/predict.plsda.Rd
mdatools/man/classify.plsda.Rd
mdatools/man/plotRMSE.pls.Rd
mdatools/man/prep.norm.Rd
mdatools/man/prep.snv.Rd
mdatools/man/prep.msc.Rd
mdatools/man/summary.plsdares.Rd
mdatools/man/plotHist.Rd
mdatools/man/plotResiduals.pca.Rd
mdatools/man/plotXCumVariance.pls.Rd
mdatools/man/plotXYLoadings.pls.Rd
mdatools/man/print.simcares.Rd
mdatools/man/plotCooman.simcam.Rd
mdatools/man/regres.Rd
mdatools/man/erfinv.Rd
mdatools/man/summary.pca.Rd
mdatools/man/pls.cal.Rd
mdatools/man/getCalibrationData.simcam.Rd
mdatools/man/selectCompNum.pca.Rd
mdatools/man/plotCumVariance.pca.Rd
mdatools/man/plotPredictions.pls.Rd
mdatools/man/plotRegcoeffs.pls.Rd
mdatools/man/pca.mvreplace.Rd
mdatools/man/crossval.Rd
mdatools/man/summary.regres.Rd
mdatools/man/People.Rd
mdatools/man/selectCompNum.Rd
mdatools/man/plotXYScores.plsres.Rd
mdatools/man/plotPredictions.regres.Rd
mdatools/man/getVIPScores.Rd
mdatools/man/plotRMSE.Rd
mdatools/man/print.pca.Rd
mdatools/man/getVIPScores.pls.Rd
mdatools/man/plotResiduals.simcam.Rd
mdatools/man/plot.pls.Rd
mdatools/man/plotVariance.pls.Rd
mdatools/man/plotPerformance.classmodel.Rd
mdatools/man/plotXYLoadings.Rd
mdatools/man/plotVariance.Rd
mdatools/man/plotSpecificity.classres.Rd
mdatools/man/ldecomp.getDistances.Rd
mdatools/man/as.matrix.regres.Rd
mdatools/man/pca.nipals.Rd
mdatools/man/print.plsda.Rd
mdatools/man/plotScores.Rd
mdatools/man/print.simca.Rd
mdatools/man/ldecomp.getResLimits.Rd
mdatools/man/print.plsdares.Rd
mdatools/man/plot.classres.Rd
mdatools/man/plot.pca.Rd
mdatools/man/plotModellingPower.simcam.Rd
mdatools/man/plotXScores.plsres.Rd
mdatools/man/print.classres.Rd