Man pages for mdatools
Multivariate Data Analysis for Chemometrics

as.matrix.classresas.matrix method for classification results
as.matrix.ldecompas.matrix method for ldecomp object
as.matrix.plsdaresas.matrix method for PLS-DA results
as.matrix.plsresas.matrix method for PLS results
as.matrix.regcoeffsas.matrix method for regression coefficients class
as.matrix.regresas.matrix method for regression results
as.matrix.simcamresas.matrix method for SIMCAM results
as.matrix.simcaresas.matrix method for SIMCA classification results
capitalizeCapitalize text or vector with text values
carbsRaman spectra of carbonhydrates
categorizeCategorize PCA results
categorize.pcaCategorize PCA results based on orthogonal and score...
categorize.plsCategorize data rows based on PLS results and critical limits...
chisq.critCalculates critical limits for distance values using...
chisq.probCalculate probabilities for distance values using Chi-square...
classify.plsdaPLS-DA classification
classify.simcaSIMCA classification
classmodel.processRefValuesCheck reference class values and convert it to a factor if...
classresResults of classification
classres.getPerformanceCalculation of classification performance parameters
confint.regcoeffsConfidence intervals for regression coefficients
constraintClass for MCR-ALS constraint
constraintAngleMethod for angle constraint
constraintClosureMethod for closure constraint
constraintNonNegativityMethod for non-negativity constraint
constraintNormMethod for normalization constraint
constraints.listShows information about all implemented constraints
constraintUnimodMethod for unimodality constraint
crossvalGenerate sequence of indices for cross-validation
crossval.getParamsDefine parameters based on 'cv' value
crossval.regmodelCross-validation of a regression model
crossval.simcaCross-validation of a SIMCA model
crossval.strString with description of cross-validation method
dd.critCalculates critical limits for distance values using Data...
ddmoments.paramCalculates critical limits for distance values using Data...
ddrobust.paramCalculates critical limits for distance values using Data...
ellipseCreate ellipse on the current plot
employ.constraintApplies constraint to a dataset
employ.prepApplies a list with preprocessing methods to a dataset
eyeCreate the identity matrix
fprintfImitation of fprinf() function
getCalibrationDataCalibration data
getCalibrationData.pcaReturns matrix with original calibration data
getCalibrationData.simcamGet calibration data
getConfidenceEllipseCompute confidence ellipse for a set of points
getConfusionMatrixConfusion matrix for classification results
getConfusionMatrix.classresConfusion matrix for classification results
getConvexHullCompute coordinates of a closed convex hull for data points
getDataLabelsCreate a vector with labels for plot series
getImplementedConstraintsShows a list with implemented constraints
getImplementedPrepMethodsShows a list with implemented preprocessing methods
getLabelsAsIndicesCreate labels as column or row indices
getLabelsAsValuesCreate labels from data values
getMainTitleGet main title
getPlotColorsDefine colors for plot series
getProbabilitiesGet class belonging probability
getProbabilities.pcaProbabilities for residual distances
getProbabilities.simcaProbabilities of class belonging for PCA/SIMCA results
getPureVariablesIdentifies pure variables
getRCreates rotation matrix to map a set vectors 'base1' to a set...
getRegcoeffsGet regression coefficients
getRegcoeffs.regmodelRegression coefficients for PLS model'
getResReturn list with valid results
getSelectedComponentsGet selected components
getSelectivityRatioSelectivity ratio
getSelectivityRatio.plsSelectivity ratio for PLS model
getVariance.mcrCompute explained variance for MCR case
getVIPScoresVIP scores
getVIPScores.plsVIP scores for PLS model
hotelling.critCalculate critical limits for distance values using Hotelling...
hotelling.probCalculate probabilities for distance values and given...
imshowshow image data as an image
iplsVariable selection with interval PLS
ipls.backwardRuns the backward iPLS algorithm
ipls.forwardRuns the forward iPLS algorithm
jm.critCalculate critical limits for distance values using...
jm.probCalculate probabilities for distance values and given...
ldecompClass for storing and visualising linear decomposition of...
ldecomp.getDistancesCompute score and residual distances
ldecomp.getLimitsCoordinatesCompute coordinates of lines or curves with critical limits
ldecomp.getLimParamsCompute parameters for critical limits based on calibration...
ldecomp.getQLimitsCompute critical limits for orthogonal distances (Q)
ldecomp.getT2LimitsCompute critical limits for score distances (T2)
ldecomp.getVariancesCompute explained variance
ldecomp.plotResidualsResiduals distance plot for a set of ldecomp objects
mcrGeneral class for Multivariate Curve Resolution model
mcralsMultivariate curve resolution using Alternating Least Squares
mcrals.calIdentifies pure variables
mcrals.fcnnlsFast combinatorial non-negative least squares
mcrals.nnlsNon-negative least squares
mcrals.olsOrdinary least squares
mcrpureMultivariate curve resolution based on pure variables
mda.cbindA wrapper for cbind() method with proper set of attributes
mda.data2imConvert data matrix to an image
mda.df2matConvert data frame to a matrix
mda.exclcolsExclude/hide columns in a dataset
mda.exclrowsExclude/hide rows in a dataset
mda.getattrGet data attributes
mda.getexclindGet indices of excluded rows or columns
mda.im2dataConvert image to data matrix
mda.inclcolsInclude/unhide the excluded columns
mda.inclrowsinclude/unhide the excluded rows
mdaplotPlotting function for a single set of objects
mdaplot.areColorsCheck color values
mdaplot.formatValuesFormat vector with numeric values
mdaplotgPlotting function for several plot series
mdaplot.getColorsColor values for plot elements
mdaplot.getXAxisLimCalculate limits for x-axis.
mdaplot.getXTickLabelsPrepare xticklabels for plot
mdaplot.getXTicksPrepare xticks for plot
mdaplot.getYAxisLimCalculate limits for y-axis.
mdaplot.getYTickLabelsPrepare yticklabels for plot
mdaplot.getYTicksPrepare yticks for plot
mdaplotg.getLegendCreate and return vector with legend values
mdaplotg.getXLimCompute x-axis limits for mdaplotg
mdaplotg.getYLimCompute y-axis limits for mdaplotg
mdaplotg.prepareDataPrepare data for mdaplotg
mdaplotg.processParamCheck mdaplotg parameters and replicate them if necessary
mdaplotg.showLegendShow legend for mdaplotg
mdaplot.plotAxesCreate axes plane
mdaplot.prepareColorsPrepare colors based on palette and opacity value
mdaplot.showColorbarPlot colorbar
mdaplot.showLinesPlot lines
mdaplotyyCreate line plot with double y-axis
mda.purgeRemoves excluded (hidden) rows and colmns from data
mda.purgeColsRemoves excluded (hidden) colmns from data
mda.purgeRowsRemoves excluded (hidden) rows from data
mda.rbindA wrapper for rbind() method with proper set of attributes
mda.setattrSet data attributes
mda.setimbgRemove background pixels from image data
mda.showWrapper for show() method
mda.subsetA wrapper for subset() method with proper set of attributed
mda.tA wrapper for t() method with proper set of attributes
mdatoolsPackage for Multivariate Data Analysis (Chemometrics)
pcaPrincipal Component Analysis
pca.calPCA model calibration
pca.getBLow-dimensional approximation of data matrix X
pca.mvreplaceReplace missing values in data
pca.nipalsNIPALS based PCA algorithm
pcaresResults of PCA decomposition
pca.runRuns one of the selected PCA methods
pca.svdSingular Values Decomposition based PCA algorithm
pcvCompute matrix with pseudo-validation set
pelletsImage data
peoplePeople data
pinvPseudo-inverse matrix
plotBarsShow plot series as bars
plotBiplotBiplot
plotBiplot.pcaPCA biplot
plot.classresPlot function for classification results
plotConfidenceEllipseAdd confidence ellipse for groups of points on scatter plot
plotContributionsPlot resolved contributions
plotContributions.mcrShow plot with resolved contributions
plotConvexHullAdd convex hull for groups of points on scatter plot
plotCoomanCooman's plot
plotCooman.simcamCooman's plot for SIMCAM model
plotCooman.simcamresCooman's plot for SIMCAM results
plotCorrCorrelation plot
plotCorr.randtestCorrelation plot for randomization test results
plotCumVarianceVariance plot
plotCumVariance.ldecompCumulative explained variance plot
plotCumVariance.mcrShow plot with cumulative explained variance
plotCumVariance.pcaCumulative explained variance plot for PCA model
plotDensityShow plot series as density plot (using hex binning)
plotDiscriminationPowerDiscrimination power plot
plotDiscriminationPower.simcamDiscrimination power plot for SIMCAM model
plotDistDoFDegrees of freedom plot for both distances
plotErrorbarsShow plot series as error bars
plotExtremeShows extreme plot for SIMCA model
plotExtreme.pcaExtreme plot
plotHistStatistic histogram
plotHist.randtestHistogram plot for randomization test results
plotHotellingEllipseHotelling ellipse
plot.iplsOverview plot for iPLS results
plotLinesShow plot series as set of lines
plotLoadingsLoadings plot
plotLoadings.pcaLoadings plot for PCA model
plot.mcrPlot summary for MCR model
plotMisclassifiedMisclassification ratio plot
plotMisclassified.classmodelMisclassified ratio plot for classification model
plotMisclassified.classresMisclassified ratio plot for classification results
plotModelDistanceModel distance plot
plotModelDistance.simcamModel distance plot for SIMCAM model
plotModellingPowerModelling power plot
plot.pcaModel overview plot for PCA
plot.pcaresPlot method for PCA results object
plotPerformanceClassification performance plot
plotPerformance.classmodelPerformance plot for classification model
plotPerformance.classresPerformance plot for classification results
plot.plsModel overview plot for PLS
plot.plsdaModel overview plot for PLS-DA
plot.plsdaresOverview plot for PLS-DA results
plot.plsresOverview plot for PLS results
plotPointsShapeAdd confidence ellipse or convex hull for group of points
plotPredictionsPredictions plot
plotPredictions.classmodelPredictions plot for classification model
plotPredictions.classresPrediction plot for classification results
plotPredictions.regmodelPredictions plot for regression model
plotPredictions.regresPredictions plot for regression results
plotPredictions.simcamPredictions plot for SIMCAM model
plotPredictions.simcamresPrediction plot for SIMCAM results
plotProbabilitiesPlot for class belonging probability
plotProbabilities.classresPlot for class belonging probability
plotPurityPlot purity values
plotPurity.mcrpurePurity values plot
plotPuritySpectraPlot purity spectra
plotPuritySpectra.mcrpurePurity spectra plot
plotQDoFDegrees of freedom plot for orthogonal distance (Nh)
plot.randtestPlot for randomization test results
plot.regcoeffsRegression coefficients plot
plotRegcoeffsRegression coefficients plot
plotRegcoeffs.regmodelRegression coefficient plot for regression model
plot.regresPlot method for regression results
plotRegressionLineAdd regression line for data points
plotResidualsResiduals plot
plotResiduals.ldecompResidual distance plot
plotResiduals.pcaResiduals distance plot for PCA model
plotResiduals.regresResiduals plot for regression results
plotRMSERMSE plot
plotRMSE.iplsRMSE development plot
plotRMSE.regmodelRMSE plot for regression model
plotRMSE.regresRMSE plot for regression results
plotScatterShow plot series as set of points
plotScoresScores plot
plotScores.ldecompScores plot
plotScores.pcaScores plot for PCA model
plotSelectionSelected intervals plot
plotSelection.iplsiPLS performance plot
plotSelectivityRatioSelectivity ratio plot
plotSelectivityRatio.plsSelectivity ratio plot for PLS model
plotSensitivitySensitivity plot
plotSensitivity.classmodelSensitivity plot for classification model
plotSensitivity.classresSensitivity plot for classification results
plotseriesCreate plot series object based on data, plot type and...
plot.simcaModel overview plot for SIMCA
plot.simcamModel overview plot for SIMCAM
plot.simcamresModel overview plot for SIMCAM results
plotSpecificitySpecificity plot
plotSpecificity.classmodelSpecificity plot for classification model
plotSpecificity.classresSpecificity plot for classification results
plotSpectraPlot resolved spectra
plotSpectra.mcrShow plot with resolved spectra
plotT2DoFDegrees of freedom plot for score distance (Nh)
plotVarianceVariance plot
plotVariance.ldecompExplained variance plot
plotVariance.mcrShow plot with explained variance
plotVariance.pcaExplained variance plot for PCA model
plotVariance.plsVariance plot for PLS
plotVariance.plsresExplained X variance plot for PLS results
plotVIPScoresVIP scores plot
plotVIPScores.plsVIP scores plot for PLS model
plotWeightsPlot for PLS weights
plotWeights.plsX loadings plot for PLS
plotXCumVarianceX cumulative variance plot
plotXCumVariance.plsCumulative explained X variance plot for PLS
plotXCumVariance.plsresExplained cumulative X variance plot for PLS results
plotXLoadingsX loadings plot
plotXLoadings.plsX loadings plot for PLS
plotXResidualsX residuals plot
plotXResiduals.plsResidual distance plot for decomposition of X data
plotXResiduals.plsresX residuals plot for PLS results
plotXScoresX scores plot
plotXScores.plsX scores plot for PLS
plotXScores.plsresX scores plot for PLS results
plotXVarianceX variance plot
plotXVariance.plsExplained X variance plot for PLS
plotXVariance.plsresExplained X variance plot for PLS results
plotXYLoadingsX loadings plot
plotXYLoadings.plsXY loadings plot for PLS
plotXYResidualsPlot for XY-residuals
plotXYResiduals.plsResidual XY-distance plot
plotXYResiduals.plsresResidual distance plot
plotXYScoresXY scores plot
plotXYScores.plsXY scores plot for PLS
plotXYScores.plsresXY scores plot for PLS results
plotYCumVarianceY cumulative variance plot
plotYCumVariance.plsCumulative explained Y variance plot for PLS
plotYCumVariance.plsresExplained cumulative Y variance plot for PLS results
plotYResidualsY residuals plot
plotYResiduals.plsresY residuals plot for PLS results
plotYResiduals.regmodelY residuals plot for regression model
plotYVarianceY variance plot
plotYVariance.plsExplained Y variance plot for PLS
plotYVariance.plsresExplained Y variance plot for PLS results
plsPartial Least Squares regression
pls.calPLS model calibration
plsdaPartial Least Squares Discriminant Analysis
plsdaresPLS-DA results
pls.getLimitsCoordinatesCompute coordinates of lines or curves with critical limits
pls.getZLimitsCompute critical limits for orthogonal distances (Q)
plsresPLS results
pls.runRuns selected PLS algorithm
pls.simplsSIMPLS algorithm
predict.mcralsMCR ALS predictions
predict.mcrpureMCR predictions
predict.pcaPCA predictions
predict.plsPLS predictions
predict.plsdaPLS-DA predictions
predict.simcaSIMCA predictions
predict.simcamSIMCA multiple classes predictions
prepClass for preprocessing object
prep.alsbasecorrBaseline correction using assymetric least squares
preparePlotDataTake dataset and prepare them for plot
prep.autoscaleAutoscale values
prepCalDataPrepares calibration data
prep.genericGeneric function for preprocessing
prep.listShows information about all implemented preprocessing...
prep.mscMultiplicative Scatter Correction transformation
prep.normNormalization
prep.ref2kmKubelka-Munk transformation
prep.savgolSavytzky-Golay filter
prep.snvStandard Normal Variate transformation
prep.transformTransformation
prep.varselVariable selection
print.classresPrint information about classification result object
print.iplsPrint method for iPLS
print.ldecompPrint method for linear decomposition
print.mcralsPrint method for mcrpure object
print.mcrpurePrint method for mcrpure object
print.pcaPrint method for PCA model object
print.pcaresPrint method for PCA results object
print.plsPrint method for PLS model object
print.plsdaPrint method for PLS-DA model object
print.plsdaresPrint method for PLS-DA results object
print.plsresprint method for PLS results object
print.randtestPrint method for randtest object
print.regcoeffsprint method for regression coefficients class
print.regmodelPrint method for PLS model object
print.regresprint method for regression results object
print.simcaPrint method for SIMCA model object
print.simcamPrint method for SIMCAM model object
print.simcamresPrint method for SIMCAM results object
print.simcaresPrint method for SIMCA results object
randtestRandomization test for PLS regression
regcoeffsRegression coefficients
regcoeffs.getStatsDistribution statistics for regression coeffificents
regresRegression results
regres.biasPrediction bias
regres.errError of prediction
regres.r2Determination coefficient
regres.rmseRMSE
regress.addattrsAdd names and attributes to matrix with statistics
regres.slopeSlope
repmatReplicate matric x
rotationMatrixToX1Creates a rotation matrix to map a vector x to [1 0 0 ... 0]
selectCompNumSelect optimal number of components for a model
selectCompNum.pcaSelect optimal number of components for PCA model
selectCompNum.plsSelect optimal number of components for PLS model
selratioSelectivity ratio calculation
setDistanceLimitsSet residual distance limits
setDistanceLimits.pcaCompute and set statistical limits for Q and T2 residual...
setDistanceLimits.plsCompute and set statistical limits for residual distances.
showDistanceLimitsShow residual distance limits
showLabelsShow labels on plot
showPredictionsPredictions
showPredictions.classresShow predicted class values
simcaSIMCA one-class classification
simcamSIMCA multiclass classification
simcam.getPerformanceStatsPerformance statistics for SIMCAM model
simcamresResults of SIMCA multiclass classification
simcaresResults of SIMCA one-class classification
simdataSpectral data of polyaromatic hydrocarbons mixing
splitExcludedDataSplit the excluded part of data
splitPlotDataSplit dataset to x and y values depending on plot type
summary.classresSummary statistics about classification result object
summary.iplsSummary for iPLS results
summary.ldecompSummary statistics for linear decomposition
summary.mcralsSummary method for mcrals object
summary.mcrpureSummary method for mcrpure object
summary.pcaSummary method for PCA model object
summary.pcaresSummary method for PCA results object
summary.plsSummary method for PLS model object
summary.plsdaSummary method for PLS-DA model object
summary.plsdaresSummary method for PLS-DA results object
summary.plsressummary method for PLS results object
summary.randtestSummary method for randtest object
summary.regcoeffsSummary method for regcoeffs object
summary.regmodelSummary method for regression model object
summary.regressummary method for regression results object
summary.simcaSummary method for SIMCA model object
summary.simcamSummary method for SIMCAM model object
summary.simcamresSummary method for SIMCAM results object
summary.simcaresSummary method for SIMCA results object
unmix.mcrpureUnmix spectral data using pure variables estimated before
vipscoresVIP scores for PLS model
mdatools documentation built on Sept. 13, 2021, 9:07 a.m.