mdatools: Multivariate Data Analysis for Chemometrics

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

AuthorSergey Kucheryavskiy
Date of publication2015-11-30 21:23:13
MaintainerSergey Kucheryavskiy <svkucheryavski@gmail.com>
LicenseGPL-3
Version0.7.0

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

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