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mdatools (version 0.5.3)

Multivariate data analysis for chemometrics

Description

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

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Version

Install

install.packages('mdatools')

Monthly Downloads

802

Version

0.5.3

License

GPL-3

Maintainer

Sergey Kucheryavskiy

Last Published

April 26th, 2014

Functions in mdatools (0.5.3)

plotMisclassified.classres

Misclassified ratio plot for classification results
mdaplot.showColorbar

Plot colorbar
plotSensitivity

Sensitivity plot
getMainTitle

Get main title
plotXVariance.plsres

Explained X variance plot for PLS results
predict.simca

SIMCA predictions
predict.pca

PCA predictions
print.regcoeffs

print method for regression coefficients class
regres.r2

Determination coefficient
print.simca

Print method for SIMCA model object
bars

Show bars on axes
plotModelDistance

Model distance plot
summary.pls

Summary method for PLS model object
plotResiduals.ldecomp

Residuals plot for linear decomposition
plotResiduals.simcares

Residuals plot for SIMCA results
errorbars

Show error bars on a plot
plotSpecificity.classres

Specificity plot for classification results
crossval

Generate sequence of indices for cross-validation
mdaplot.showLabels

Plot labels Shows labels for data elements (points, bars) on a plot.
classres

Results of classification
plot.plsdares

Overview plot for PLS-DA results
plotPerformance.classres

Performance plot for classification results
plotXLoadings

X loadings plot
plotXVariance.pls

Explained X variance plot for PLS
plotXYLoadings.pls

XY loadings plot for PLS
plsdares

PLS-DA results
plotYResiduals.pls

Y residuals plot for PLS
getSelectivityRatio.pls

Selectivity ratio for PLS model
as.matrix.regcoeffs

as.matrix method for regression coefficients class
regres.slope

Slope
getVIPScores

VIP scores
classify.plsda

PLS-DA classification
mdaplot.getColors

Color values for plot elements
regcoeffs

Regression coefficients
getCalibrationData.simcam

Get calibration data
plotCumVariance.pca

Cumulative explained variance plot for PCA
plot.pca

Model overview plot for PCA
summary.pcares

Summary method for PCA results object
plotCooman

Cooman's plot
selectCompNum.pls

Select optimal number of components for PLS model
plotScores.pca

Scores plot for PCA
mdaplot.formatValues

Format vector with numeric values
summary.pca

Summary method for PCA model object
plotXResiduals.pls

X residuals plot for PLS
erfinv

Inverse error function
summary.plsdares

Summary method for PLS-DA results object
plotMisclassified

Misclassification ratio plot
mdaplot.showGrid

Plot grid
plotRMSE.pls

RMSE plot for PLS
plotPredictions.classres

Prediction plot for classification results
pca.svd

Singular Values Decomposition based PCA algorithm
plotXYLoadings

X loadings plot
summary.simcares

Summary method for SIMCA results object
plotXScores.pls

X scores plot for PLS
simca

SIMCA one-class classification
plot.simca

Model overview plot for SIMCA
plotYCumVariance.pls

Cumulative explained Y variance plot for PLS
people

People data
pls

Partial Least Squares regression
pls.calculateVIPScores

VIP scores calculation for PLS model
pls.simpls

SIMPLS algorithm
as.matrix.ldecomp

as.matrix method for ldecomp object
print.regres

print method for regression results object
plot.regcoeffs

Regression coefficients plot
ldecomp.getVariances

Explained variance for linear decomposition
summary.simcamres

Summary method for SIMCAM results object
plotDiscriminationPower.simcam

Discrimination power plot for SIMCAM model
pca.crossval

Cross-validation of a PCA model
mdaplot.areColors

Check color values
plotSensitivity.classmodel

Sensitivity plot for classification model
simcares

Results of SIMCA one-class classification
print.pcares

Print method for PCA results object
simdata

Spectral data of polyaromatic hydrocarbons mixing
plotResiduals.simcamres

Residuals plot for SIMCAM results
plot.pcares

Pplot method for PCA results object
simcam.getPerformanceStatistics

Performance statistics for SIMCAM model
plotDiscriminationPower

Discrimination power plot
plsda.crossval

Cross-validation of a PLS-DA model
mdaplot.getAxesLim

Calculate axes limits
getCalibrationData.pca

Get calibration data
prep.autoscale

Autoscale values
plotCumVariance.ldecomp

Cumulative explained variance plot for linear decomposition
as.matrix.plsres

as.matrix method for PLS results
print.simcam

Print method for SIMCAM model object
plotXCumVariance.pls

Cumulative explained X variance plot for PLS
plotYCumVariance

Y cumulative variance plot
predict.pls

PLS predictions
plotPredictions.pls

Predictions plot for PLS
plotScores.ldecomp

Scores plot for linear decomposition
plotModellingPower.simca

Modelling power plot for SIMCA model
plotRegcoeffs.pls

Regression coefficient plot for PLS
plotYCumVariance.plsres

Explained cumulative Y variance plot for PLS results
ldecomp.getResLimits

Statistical limits for Q2 and T2 residuals
plot.plsres

Overview plot for PLS results
mdaplot.plotAxes

Create axes plane
plotSelectivityRatio.pls

Selectivity ratio plot for PLS model
plotSelectivityRatio

Selectivity ratio plot
plotXYScores.pls

XY scores plot for PLS
plsres

PLS results
pls.crossval

Cross-validation of a PLS model
summary.plsres

summary method for PLS results object
predict.plsda

PLS-DA predictions
plotResiduals

Residuals plot
pca

Principal Component Analysis
pcares

Results of PCA decomposition
plotCooman.simcamres

Cooman's plot for SIMCAM results
pca.nipals

NIPALS based PCA algorithm
regres.bias

Prediction bias
plotModellingPower

Modelling power plot
plotCumVariance

Variance plot
plotXCumVariance

X cumulative variance plot
print.plsres

print method for PLS results object
plotVariance

Variance plot
plotXCumVariance.plsres

Explained cumulative X variance plot for PLS results
plotVIPScores

VIP scores plot
plotVariance.ldecomp

Explained variance plot for linear decomposition
plotCooman.simcam

Cooman's plot for SIMCAM model
simca.classify

SIMCA classification
summary.simcam

Summary method for SIMCAM model object
summary.plsda

Summary method for PLS-DA model object
plotVariance.pls

Variance plot for PLS
plotPerformance

Classification performance plot
regres

Regression results
plotYVariance.plsres

Explained Y variance plot for PLS results
plotXLoadings.pls

X loadings plot for PLS
print.simcares

Print method for SIMCA results object
plotXVariance

X variance plot
print.plsdares

Print method for PLS-DA results object
pls.cal

PLS model calibration
showPredictions.classres

Show predicted class values
plsda

Partial Least Squares Discriminant Analysis
getClassificationPerformance

Calculation of classification performance parameters
prep.snv

Standard Normal Variate transformation
showPredictions

Predictions
getVIPScores.pls

VIP scores for PLS model
simcamres

Results of SIMCA multiclass classification
as.matrix.regres

as.matrix method for regression results
summary.simca

Summary method for SIMCA model object
plotModelDistance.simcam

Modelling distance plot for SIMCAM model
simcam

SIMCA multiclass classification
plotXResiduals

X residuals plot
mdatools

Package for Multivariate Data Analysis (Chemometrics)
summary.regres

summary method for regression results object
plot.regres

plot method for regression results
as.matrix.classres

as.matrix method for classification results
plotSpecificity

Specificity plot
plotPredictions.plsres

Predictions plot for PLS results
mdaplotg

Plotting function for several sets of objects
plotXYScores

XY scores plot
pls.calculateSelectivityRatio

Selectivity ratio calculation
plotXResiduals.plsres

X residuals plot for PLS results
plotYResiduals.regres

Residuals plot for regression results
getSelectedComponents.classres

Get selected components
as.matrix.plsdares

as.matrix method for PLS-DA results
print.pls

Print method for PLS model object
plotYVariance.pls

Explained Y variance plot for PLS
ldecomp.getDistances

Residuals distances for linear decomposition
getSelectivityRatio

Selectivity ratio
pca.mvreplace

Replace missing values in data
mdaplot.showRegressionLine

Regression line for data points
ldecomp

Linear decomposition of data
plot.simcamres

Model overview plot for SIMCAM results
pca.cal

PCA model calibration
plot.simcam

Model overview plot for SIMCAM
mdaplot.showLines

Plot lines
prep.msc

Multiplicative Scatter Correction transformation
regres.rmse

RMSE
pinv

Pseudo-inverse matrix
plot.pls

Model overview plot for PLS
summary.classres

Summary statistics about classification result object
plotPredictions.regres

Predictions plot for regression results
print.plsda

Print method for PLS-DA model object
summary.ldecomp

Summary statistics for linear decomposition
plotRMSE.plsres

RMSE plot for PLS results
plotModellingPower.simcam

Modelling power plot for SIMCAM model
plotRegcoeffs

Regression coefficients plot
selectCompNum.pca

Select optimal number of components for PCA model
plotPredictions

Predictions plot
plotSensitivity.classres

Sensitivity plot for classification results
plotVIPScores.pls

VIP scores plot for PLS model
plotResiduals.simcam

Residuals plot for SIMCAM model
plotXYScores.plsres

XY scores plot for PLS results
plotScores

Scores plot
getCalibrationData

Calibration data
plotSpecificity.classmodel

Specificity plot for classification model
plot.classres

Plot function for classification results
plotYVariance

Y variance plot
simca.crossval

Cross-validation of a SIMCA model
plotXScores

X scores plot
plotLoadings

Loadings plot
plsda.getReferenceValues

Reference values for PLS-DA
plotMisclassified.classmodel

Misclassified ratio plot for classification model
predict.simcam

SIMCA multiple classes predictions
print.ldecomp

Print method for linear decomposition
plot.plsda

Model overview plot for PLS-DA
plotRMSE

RMSE plot
plotPerformance.classmodel

Performance plot for classification model
plotLoadings.pca

Loadings plot for PCA
plotRMSE.regres

RMSE plot for regression results
plotResiduals.pca

Residuals plot for PCA
plotVariance.pca

Explained variance plot for PCA
getSelectedComponents

Get selected components
print.classres

Print information about classification result object
mdaplot

Plotting function for a single set of objects
print.pca

Print method for PCA model object
selectCompNum

Select optimal number of components for a model
regcoeffs.getStat

Confidence intervals and p-values for regression coeffificents
mdaplot.showLegend

Plot legend
plotPredictions.classmodel

Predictions plot for classification model
plotXScores.plsres

X scores plot for PLS results
plotYResiduals

Y residuals plot
prep.savgol

Savytzky-Golay filter
print.simcamres

Print method for SIMCAM results object