├── .github ├── FUNDING.yml └── workflows │ └── test-package.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── classmodel.R ├── classres.R ├── constraints.R ├── crossval.R ├── defaults.R ├── ipls.R ├── ldecomp.R ├── mcr.R ├── mcrals.R ├── mcrpure.R ├── mdaplot.R ├── mdaplotg.R ├── misc.R ├── pca.R ├── pcares.R ├── plotseries.R ├── pls.R ├── plsda.R ├── plsdares.R ├── plsres.R ├── prep.R ├── randtest.R ├── regcoeffs.R ├── regmodel.R ├── regres.R ├── simca.R ├── simcam.R ├── simcamres.R └── simcares.R ├── README.md ├── data ├── carbs.RData ├── pellets.RData ├── people.RData └── simdata.RData ├── inst └── CITATION ├── man ├── as.matrix.classres.Rd ├── as.matrix.ldecomp.Rd ├── as.matrix.plsdares.Rd ├── as.matrix.plsres.Rd ├── as.matrix.regcoeffs.Rd ├── as.matrix.regres.Rd ├── as.matrix.simcamres.Rd ├── as.matrix.simcares.Rd ├── capitalize.Rd ├── carbs.Rd ├── categorize.Rd ├── categorize.pca.Rd ├── categorize.pls.Rd ├── chisq.crit.Rd ├── chisq.prob.Rd ├── classify.plsda.Rd ├── classify.simca.Rd ├── classmodel.processRefValues.Rd ├── classres.Rd ├── classres.getPerformance.Rd ├── confint.regcoeffs.Rd ├── constraint.Rd ├── constraintAngle.Rd ├── constraintClosure.Rd ├── constraintNonNegativity.Rd ├── constraintNorm.Rd ├── constraintUnimod.Rd ├── constraints.list.Rd ├── crossval.Rd ├── crossval.getParams.Rd ├── crossval.regmodel.Rd ├── crossval.simca.Rd ├── crossval.str.Rd ├── dd.crit.Rd ├── ddmoments.param.Rd ├── ddrobust.param.Rd ├── ellipse.Rd ├── employ.constraint.Rd ├── employ.prep.Rd ├── fprintf.Rd ├── getCalibrationData.Rd ├── getCalibrationData.pca.Rd ├── getCalibrationData.simcam.Rd ├── getConfidenceEllipse.Rd ├── getConfusionMatrix.Rd ├── getConfusionMatrix.classres.Rd ├── getConvexHull.Rd ├── getDataLabels.Rd ├── getImplementedConstraints.Rd ├── getImplementedPrepMethods.Rd ├── getLabelsAsIndices.Rd ├── getLabelsAsValues.Rd ├── getMainTitle.Rd ├── getPlotColors.Rd ├── getProbabilities.Rd ├── getProbabilities.pca.Rd ├── getProbabilities.simca.Rd ├── getPureVariables.Rd ├── getRegcoeffs.Rd ├── getRegcoeffs.regmodel.Rd ├── getRes.Rd ├── getSelectedComponents.Rd ├── getSelectivityRatio.Rd ├── getSelectivityRatio.pls.Rd ├── getVIPScores.Rd ├── getVIPScores.pls.Rd ├── getVariance.mcr.Rd ├── hotelling.crit.Rd ├── hotelling.prob.Rd ├── imshow.Rd ├── ipls.Rd ├── ipls.backward.Rd ├── ipls.forward.Rd ├── jm.crit.Rd ├── jm.prob.Rd ├── ldecomp.Rd ├── ldecomp.getDistances.Rd ├── ldecomp.getLimParams.Rd ├── ldecomp.getLimitsCoordinates.Rd ├── ldecomp.getQLimits.Rd ├── ldecomp.getT2Limits.Rd ├── ldecomp.getVariances.Rd ├── ldecomp.plotResiduals.Rd ├── mcr.Rd ├── mcrals.Rd ├── mcrals.cal.Rd ├── mcrals.fcnnls.Rd ├── mcrals.nnls.Rd ├── mcrals.ols.Rd ├── mcrpure.Rd ├── mda.cbind.Rd ├── mda.data2im.Rd ├── mda.df2mat.Rd ├── mda.exclcols.Rd ├── mda.exclrows.Rd ├── mda.getattr.Rd ├── mda.getexclind.Rd ├── mda.im2data.Rd ├── mda.inclcols.Rd ├── mda.inclrows.Rd ├── mda.purge.Rd ├── mda.purgeCols.Rd ├── mda.purgeRows.Rd ├── mda.rbind.Rd ├── mda.setattr.Rd ├── mda.setimbg.Rd ├── mda.show.Rd ├── mda.subset.Rd ├── mda.t.Rd ├── mdaplot.Rd ├── mdaplot.areColors.Rd ├── mdaplot.formatValues.Rd ├── mdaplot.getColors.Rd ├── mdaplot.getXAxisLim.Rd ├── mdaplot.getXTickLabels.Rd ├── mdaplot.getXTicks.Rd ├── mdaplot.getYAxisLim.Rd ├── mdaplot.getYTickLabels.Rd ├── mdaplot.getYTicks.Rd ├── mdaplot.plotAxes.Rd ├── mdaplot.prepareColors.Rd ├── mdaplot.showColorbar.Rd ├── mdaplot.showLines.Rd ├── mdaplotg.Rd ├── mdaplotg.getLegend.Rd ├── mdaplotg.getXLim.Rd ├── mdaplotg.getYLim.Rd ├── mdaplotg.prepareData.Rd ├── mdaplotg.processParam.Rd ├── mdaplotg.showLegend.Rd ├── mdaplotyy.Rd ├── mdatools.Rd ├── pca.Rd ├── pca.cal.Rd ├── pca.getB.Rd ├── pca.mvreplace.Rd ├── pca.nipals.Rd ├── pca.run.Rd ├── pca.svd.Rd ├── pcares.Rd ├── pellets.Rd ├── people.Rd ├── pinv.Rd ├── plot.classres.Rd ├── plot.ipls.Rd ├── plot.mcr.Rd ├── plot.pca.Rd ├── plot.pcares.Rd ├── plot.pls.Rd ├── plot.plsda.Rd ├── plot.plsdares.Rd ├── plot.plsres.Rd ├── plot.randtest.Rd ├── plot.regcoeffs.Rd ├── plot.regres.Rd ├── plot.simca.Rd ├── plot.simcam.Rd ├── plot.simcamres.Rd ├── plotBars.Rd ├── plotBiplot.Rd ├── plotBiplot.pca.Rd ├── plotConfidenceEllipse.Rd ├── plotContributions.Rd ├── plotContributions.mcr.Rd ├── plotConvexHull.Rd ├── plotCooman.Rd ├── plotCooman.simcam.Rd ├── plotCooman.simcamres.Rd ├── plotCorr.Rd ├── plotCorr.randtest.Rd ├── plotCumVariance.Rd ├── plotCumVariance.ldecomp.Rd ├── plotCumVariance.mcr.Rd ├── plotCumVariance.pca.Rd ├── plotDensity.Rd ├── plotDiscriminationPower.Rd ├── plotDiscriminationPower.simcam.Rd ├── plotDistDoF.Rd ├── plotErrorbars.Rd ├── plotExtreme.Rd ├── plotExtreme.pca.Rd ├── plotHist.Rd ├── plotHist.randtest.Rd ├── plotHotellingEllipse.Rd ├── plotLines.Rd ├── plotLoadings.Rd ├── plotLoadings.pca.Rd ├── plotMisclassified.Rd ├── plotMisclassified.classmodel.Rd ├── plotMisclassified.classres.Rd ├── plotModelDistance.Rd ├── plotModelDistance.simcam.Rd ├── plotModellingPower.Rd ├── plotPerformance.Rd ├── plotPerformance.classmodel.Rd ├── plotPerformance.classres.Rd ├── plotPointsShape.Rd ├── plotPredictions.Rd ├── plotPredictions.classmodel.Rd ├── plotPredictions.classres.Rd ├── plotPredictions.regmodel.Rd ├── plotPredictions.regres.Rd ├── plotPredictions.simcam.Rd ├── plotPredictions.simcamres.Rd ├── plotProbabilities.Rd ├── plotProbabilities.classres.Rd ├── plotPurity.Rd ├── plotPurity.mcrpure.Rd ├── plotPuritySpectra.Rd ├── plotPuritySpectra.mcrpure.Rd ├── plotQDoF.Rd ├── plotRMSE.Rd ├── plotRMSE.ipls.Rd ├── plotRMSE.regmodel.Rd ├── plotRMSE.regres.Rd ├── plotRMSERatio.Rd ├── plotRMSERatio.regmodel.Rd ├── plotRegcoeffs.Rd ├── plotRegcoeffs.regmodel.Rd ├── plotRegressionLine.Rd ├── plotResiduals.Rd ├── plotResiduals.ldecomp.Rd ├── plotResiduals.pca.Rd ├── plotResiduals.regres.Rd ├── plotScatter.Rd ├── plotScores.Rd ├── plotScores.ldecomp.Rd ├── plotScores.pca.Rd ├── plotSelection.Rd ├── plotSelection.ipls.Rd ├── plotSelectivityRatio.Rd ├── plotSelectivityRatio.pls.Rd ├── plotSensitivity.Rd ├── plotSensitivity.classmodel.Rd ├── plotSensitivity.classres.Rd ├── plotSpecificity.Rd ├── plotSpecificity.classmodel.Rd ├── plotSpecificity.classres.Rd ├── plotSpectra.Rd ├── plotSpectra.mcr.Rd ├── plotT2DoF.Rd ├── plotVIPScores.Rd ├── plotVIPScores.pls.Rd ├── plotVariance.Rd ├── plotVariance.ldecomp.Rd ├── plotVariance.mcr.Rd ├── plotVariance.pca.Rd ├── plotVariance.pls.Rd ├── plotVariance.plsres.Rd ├── plotWeights.Rd ├── plotWeights.pls.Rd ├── plotXCumVariance.Rd ├── plotXCumVariance.pls.Rd ├── plotXCumVariance.plsres.Rd ├── plotXLoadings.Rd ├── plotXLoadings.pls.Rd ├── plotXResiduals.Rd ├── plotXResiduals.pls.Rd ├── plotXResiduals.plsres.Rd ├── plotXScores.Rd ├── plotXScores.pls.Rd ├── plotXScores.plsres.Rd ├── plotXVariance.Rd ├── plotXVariance.pls.Rd ├── plotXVariance.plsres.Rd ├── plotXYLoadings.Rd ├── plotXYLoadings.pls.Rd ├── plotXYResiduals.Rd ├── plotXYResiduals.pls.Rd ├── plotXYResiduals.plsres.Rd ├── plotXYScores.Rd ├── plotXYScores.pls.Rd ├── plotXYScores.plsres.Rd ├── plotYCumVariance.Rd ├── plotYCumVariance.pls.Rd ├── plotYCumVariance.plsres.Rd ├── plotYResiduals.Rd ├── plotYResiduals.plsres.Rd ├── plotYResiduals.regmodel.Rd ├── plotYVariance.Rd ├── plotYVariance.pls.Rd ├── plotYVariance.plsres.Rd ├── plotseries.Rd ├── pls.Rd ├── pls.cal.Rd ├── pls.getLimitsCoordinates.Rd ├── pls.getZLimits.Rd ├── pls.getpredictions.Rd ├── pls.getxdecomp.Rd ├── pls.getxscores.Rd ├── pls.getydecomp.Rd ├── pls.getyscores.Rd ├── pls.run.Rd ├── pls.simpls.Rd ├── pls.simplsold.Rd ├── plsda.Rd ├── plsdares.Rd ├── plsres.Rd ├── predict.mcrals.Rd ├── predict.mcrpure.Rd ├── predict.pca.Rd ├── predict.pls.Rd ├── predict.plsda.Rd ├── predict.simca.Rd ├── predict.simcam.Rd ├── prep.Rd ├── prep.alsbasecorr.Rd ├── prep.autoscale.Rd ├── prep.generic.Rd ├── prep.list.Rd ├── prep.msc.Rd ├── prep.norm.Rd ├── prep.ref2km.Rd ├── prep.savgol.Rd ├── prep.snv.Rd ├── prep.transform.Rd ├── prep.varsel.Rd ├── prepCalData.Rd ├── preparePlotData.Rd ├── print.classres.Rd ├── print.ipls.Rd ├── print.ldecomp.Rd ├── print.mcrals.Rd ├── print.mcrpure.Rd ├── print.pca.Rd ├── print.pcares.Rd ├── print.pls.Rd ├── print.plsda.Rd ├── print.plsdares.Rd ├── print.plsres.Rd ├── print.randtest.Rd ├── print.regcoeffs.Rd ├── print.regmodel.Rd ├── print.regres.Rd ├── print.simca.Rd ├── print.simcam.Rd ├── print.simcamres.Rd ├── print.simcares.Rd ├── randtest.Rd ├── regcoeffs.Rd ├── regcoeffs.getStats.Rd ├── regres.Rd ├── regres.bias.Rd ├── regres.err.Rd ├── regres.r2.Rd ├── regres.rmse.Rd ├── regres.slope.Rd ├── regress.addattrs.Rd ├── repmat.Rd ├── selectCompNum.Rd ├── selectCompNum.pca.Rd ├── selectCompNum.pls.Rd ├── selratio.Rd ├── setDistanceLimits.Rd ├── setDistanceLimits.pca.Rd ├── setDistanceLimits.pls.Rd ├── showDistanceLimits.Rd ├── showLabels.Rd ├── showPredictions.Rd ├── showPredictions.classres.Rd ├── simca.Rd ├── simcam.Rd ├── simcam.getPerformanceStats.Rd ├── simcamres.Rd ├── simcares.Rd ├── simdata.Rd ├── splitExcludedData.Rd ├── splitPlotData.Rd ├── summary.classres.Rd ├── summary.ipls.Rd ├── summary.ldecomp.Rd ├── summary.mcrals.Rd ├── summary.mcrpure.Rd ├── summary.pca.Rd ├── summary.pcares.Rd ├── summary.pls.Rd ├── summary.plsda.Rd ├── summary.plsdares.Rd ├── summary.plsres.Rd ├── summary.randtest.Rd ├── summary.regcoeffs.Rd ├── summary.regmodel.Rd ├── summary.regres.Rd ├── summary.simca.Rd ├── summary.simcam.Rd ├── summary.simcamres.Rd ├── summary.simcares.Rd ├── unmix.mcrpure.Rd └── vipscores.Rd └── tests ├── testthat.R └── testthat ├── Beer.csv ├── People.csv ├── pls-coeffs.csv ├── pls-expvar.csv ├── pls-vipscores.csv ├── pls-weight.csv ├── pls-weights.csv ├── pls-xloadings.csv ├── pls-xres.csv ├── pls-xscores.csv ├── pls-yloadings.csv ├── pls-yres.csv ├── pls-yscores.csv ├── pls2-vipscores.csv ├── plstlbx-people-weights.csv ├── plstlbx-people-xhdist.csv ├── plstlbx-people-xloadings.csv ├── plstlbx-people-xqdist.csv ├── plstlbx-people-xscores.csv ├── plstlbx-people-ypred.csv ├── 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