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
getB                    Low-dimensional approximation of data matrix X
getCalibrationData      Calibration data
getCalibrationData.pca
                        Get calibration data
getCalibrationData.simcam
                        Get calibration data
getClassificationPerformance
                        Calculation of classification performance
                        parameters
getConfusionMatrix      Confusion matrix for classification results
getConfusionMatrix.classres
                        Confusion matrix for classification results
getMainTitle            Get main title
getProbabilities        Get class belonging probability
getProbabilities.simca
                        Probability of class belonging for PCA/SIMCA
                        results
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
imshow                  show image data as an image
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.getVariances    Explained variance for linear decomposition
ldecomp.plotLimits      Shows lines with critical limits on residuals
                        plot
mda.cbind               A wrapper for cbind() method with proper set of
                        attributes
mda.data2im             Convert data matrix to an image
mda.df2mat              Convert data frame to a matrix
mda.exclcols            Exclude/hide columns in a dataset
mda.exclrows            Exclude/hide rows in a dataset
mda.getattr             Get data attributes
mda.getexclind          Get indices of excluded rows or columns
mda.im2data             Convert image to data matrix
mda.inclcols            Include/unhide the excluded columns
mda.inclrows            include/unhide the excluded rows
mda.rbind               A wrapper for rbind() method with proper set of
                        attributes
mda.setattr             Set data attributes
mda.setimbg             Remove background pixels from image data
mda.show                Wrapper for show() method
mda.subset              A wrapper for subset() method with proper set
                        of attributed
mda.t                   A wrapper for t() method with proper set of
                        attributes
mdaplot                 Plotting function for a single set of objects
mdaplot.areColors       Check color values
mdaplot.formatValues    Format vector with numeric values
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 a plot.
mdaplot.showLegend      Plot legend
mdaplot.showLines       Plot lines
mdaplot.showRegressionLine
                        Regression line for data points
mdaplotg                Plotting function for several sets of objects
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
pca.run                 Runs one of the selected PCA methods
pca.svd                 Singular Values Decomposition based PCA
                        algorithm
pcares                  Results of PCA decomposition
pellets                 Image data
people                  People data
pinv                    Pseudo-inverse matrix
plot.classres           Plot function for classification results
plot.ipls               Overview plot for iPLS results
plot.pca                Model overview plot for PCA
plot.pcares             Plot method for PCA results object
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
plot.randtest           Plot for randomization test results
plot.regcoeffs          Regression coefficients plot
plot.regres             plot method for regression results
plot.simca              Model overview plot for SIMCA
plot.simcam             Model overview plot for SIMCAM
plot.simcamres          Model overview plot for SIMCAM results
plotBiplot              Biplot
plotBiplot.pca          PCA biplot
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
plotExtreme             Shows extreme plot for SIMCA model
plotExtreme.simca       Shows extreme plot for SIMCA model
plotHist                Statistic histogram
plotHist.randtest       Histogram plot for randomization test 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
plotPerformance         Classification performance plot
plotPerformance.classmodel
                        Performance plot for classification model
plotPerformance.classres
                        Performance plot for classification 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
plotProbabilities       Plot for class belonging probability
plotProbabilities.classres
                        Plot for class belonging probability
plotRMSE                RMSE plot
plotRMSE.ipls           RMSE development plot
plotRMSE.pls            RMSE plot for PLS
plotRMSE.regres         RMSE plot for regression results
plotRegcoeffs           Regression coefficients plot
plotRegcoeffs.pls       Regression coefficient plot for PLS
plotResiduals           Residuals plot
plotResiduals.ldecomp   Residuals plot for linear decomposition
plotResiduals.pca       Residuals plot for PCA
plotResiduals.pcares    Residuals plot for PCA results
plotResiduals.simcam    Residuals plot for SIMCAM model
plotResiduals.simcamres
                        Residuals plot for SIMCAM results
plotResiduals.simcares
                        Residuals plot for SIMCA 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
plotSpecificity         Specificity plot
plotSpecificity.classmodel
                        Specificity plot for classification model
plotSpecificity.classres
                        Specificity plot for classification results
plotVIPScores           VIP scores plot
plotVIPScores.pls       VIP scores plot for PLS model
plotVariance            Variance plot
plotVariance.ldecomp    Explained variance plot for linear
                        decomposition
plotVariance.pca        Explained variance plot for PCA
plotVariance.pls        Variance plot for PLS
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
pls.run                 Runs selected PLS algorithm
pls.simpls              SIMPLS algorithm
plsda                   Partial Least Squares Discriminant Analysis
plsda.cal               Calibrate PLS-DA model
plsda.crossval          Cross-validation of a PLS-DA model
plsdares                PLS-DA results
plsres                  PLS results
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 coeffificents
regres                  Regression results
regres.bias             Prediction bias
regres.r2               Determination coefficient
regres.rmse             RMSE
regres.slope            Slope
reslim.chisq            Calculates critical limits or statistic values
                        for Q-residuals using Chi-squared distribution
reslim.dd               Statistical limits for Q and T2 residuals using
                        Data Driven approach
reslim.hotelling        Calculates critical limits for T2-residuals
                        using Hotelling T2 distribution
reslim.jm               Calculates critical limits for Q-residuals
                        using classic JM approach
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
setResLimits            Set residual limits for PCA model
setResLimits.pca        Set statistical limits for Q and T2 residuals
                        for PCA 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
                        @description 'simcares' is used to store
                        results for 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.regcoeffs       Summary method for regcoeffs 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
