R/defaults.R

Defines functions plotCorr plotHist plotXYLoadings plotXLoadings plotVariance plotResiduals plotRegcoeffs plotPredictions plotLoadings plotYCumVariance plotXCumVariance plotCumVariance plotRMSE plotSelection plotXYScores plotXScores plotScores plotBiplot plotYVariance plotXVariance plotYResiduals plotXResiduals showPredictions plotPerformance plotSensitivity plotSpecificity plotMisclassified plotModellingPower getCalibrationData plotDiscriminationPower plotModelDistance plotCooman selectCompNum getSelectivityRatio plotSelectivityRatio getVIPScores plotVIPScores getRegcoeffs plotExtreme setResLimits getProbabilities plotProbabilities getConfusionMatrix

Documented in getCalibrationData getConfusionMatrix getProbabilities getRegcoeffs getSelectivityRatio getVIPScores plotBiplot plotCooman plotCorr plotCumVariance plotDiscriminationPower plotExtreme plotHist plotLoadings plotMisclassified plotModelDistance plotModellingPower plotPerformance plotPredictions plotProbabilities plotRegcoeffs plotResiduals plotRMSE plotScores plotSelection plotSelectivityRatio plotSensitivity plotSpecificity plotVariance plotVIPScores plotXCumVariance plotXLoadings plotXResiduals plotXScores plotXVariance plotXYLoadings plotXYScores plotYCumVariance plotYResiduals plotYVariance selectCompNum setResLimits showPredictions

#' Confusion matrix for classification results
#' 
#' @details 
#' Returns confusion matrix for classification results represented by the object.
#' 
#' @param obj
#' classification results (object of class \code{simcares}, \code{simcamres}, etc)
#' @param ...
#' other parameters.
#' 
#' @export
getConfusionMatrix = function(obj, ...) {
   UseMethod("getConfusionMatrix")
}  

#' Plot for class belonging probability
#' 
#' @description
#' Makes a plot with class belonging probabilities for each object of the classification results. 
#' Works only with classification methods, which compute this probability (e.g. SIMCA). 
#' 
#' @param obj
#' an object with classification results (e.g. SIMCA)
#' @param ...
#' other parameters
#' 
#' @export
plotProbabilities = function(obj, ...) {
   UseMethod("plotProbabilities")
}  

#' Get class belonging probability
#' 
#' @description
#' Compute class belonging probabilities for classification results.
#' 
#' @param obj
#' an object with classification results (e.g. SIMCA)
#' @param ...
#' other parameters
#' 
#' @export
getProbabilities = function(obj, ...) {
   UseMethod("getProbabilities")
}  

#' Set residual limits for PCA model
#' 
#' @description
#' Calculates and set critical limits for residuals of PCA model
#' 
#' @param obj
#' a SIMCA model
#' @param ...
#' other parameters
#' 
#' @export
setResLimits = function(obj, ...) {
   UseMethod("setResLimits")
}  


#' Shows extreme plot for SIMCA model
#' 
#' @description
#' Generic function for creating extreme plot for SIMCA model
#' 
#' @param obj
#' a SIMCA model
#' @param ...
#' other parameters
#' 
#' @export
plotExtreme = function(obj, ...) {
   UseMethod("plotExtreme")
}  

#' Get regression coefficients
#' 
#' @description
#' Generic function for getting regression coefficients from PLS model
#' 
#' @param obj
#' a PLS model
#' @param ...
#' other parameters
#' 
#' @export
getRegcoeffs = function(obj, ...) {
   UseMethod("getRegcoeffs")
}  

#' VIP scores plot
#' 
#' @description
#' Generic function for plotting VIP scores values for regression model (PCR, PLS, etc)
#' 
#' @param obj
#' a regression model
#' @param ...
#' other parameters
#' 
#' @export
plotVIPScores = function(obj, ...) {
   UseMethod("plotVIPScores")
}  

#' VIP scores 
#' 
#' @description
#' Generic function for returning VIP scores values for regression model (PCR, PLS, etc)
#' 
#' @param obj
#' a regression model
#' @param ...
#' other parameters
#' 
#' @export
getVIPScores = function(obj, ...) {
   UseMethod("getVIPScores")
}  

#' Selectivity ratio plot
#' 
#' @description
#' Generic function for plotting selectivity ratio values for regression model (PCR, PLS, etc)
#' 
#' @param obj
#' a regression model
#' @param ...
#' other parameters
#' 
#' @export
plotSelectivityRatio = function(obj, ...) {
   UseMethod("plotSelectivityRatio")
}  

#' Selectivity ratio 
#' 
#' @description
#' Generic function for returning selectivity ratio values for regression model (PCR, PLS, etc)
#' 
#' @param obj
#' a regression model
#' @param ...
#' other parameters
#' 
#' @export
getSelectivityRatio = function(obj, ...) {
   UseMethod("getSelectivityRatio")
}  

#' Select optimal number of components for a model
#' 
#' @description
#' Generic function for selecting number of components for multivariate models (e.g. PCA, PLS, ...)
#' 
#' @param model
#' a model object
#' @param ncomp
#' number of components to select
#' 
#' @export
selectCompNum = function(model, ncomp) {   
   UseMethod("selectCompNum")
}   

#' Cooman's plot
#' 
#' @details
#' Generic function for Cooman's plot
#' 
#' @param obj
#' classification model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotCooman = function(obj, ...)
{
   UseMethod("plotCooman")
}

#' Model distance plot
#' 
#' @details
#' Generic function for plotting distance from object to a multivariate model
#' 
#' @param obj
#' a model object
#' @param ...
#' other arguments
#' 
#' @export
plotModelDistance = function(obj, ...)
{
   UseMethod("plotModelDistance")
}

#' Discrimination power plot
#' 
#' @details
#' Generic function for plotting discrimination power values for classification model
#' 
#' @param obj
#' a model object
#' @param ...
#' other arguments
#' 
#' @export
plotDiscriminationPower = function(obj, ...)
{
   UseMethod("plotDiscriminationPower")      
}  

#' Calibration data
#' 
#' @details
#' Generic function getting calibration data from a linear decomposition model (e.g. PCA)
#' 
#' @param obj
#' a model object
#' @param ...
#' other arguments
#' 
#' @export
getCalibrationData = function(obj, ...)
{
   UseMethod("getCalibrationData")   
}  

#' Modelling power plot
#' 
#' @details
#' Generic function for plotting modelling power values for classification model
#' 
#' @param obj
#' a model object
#' @param ...
#' other arguments
#' 
#' @export
plotModellingPower = function(obj, ...)
{
   UseMethod("plotModellingPower")   
}  

#' Misclassification ratio plot
#' 
#' @details
#' Generic function for plotting missclassification values for classification model or results
#' 
#' @param obj
#' a model or a result object
#' @param ...
#' other arguments
#' 
#' @export
plotMisclassified = function(obj, ...)
{
   UseMethod('plotMisclassified')
}

#' Specificity plot
#' 
#' @details
#' Generic function for plotting specificity values for classification model or results
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotSpecificity = function(obj, ...)
{
   UseMethod("plotSpecificity")   
}  

#' Sensitivity plot
#' 
#' @details
#' Generic function for plotting sensitivity values for classification model or results
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotSensitivity = function(obj, ...)
{
   UseMethod("plotSensitivity")   
}

#' Classification performance plot
#' 
#' @details
#' Generic function for plotting classification performance for model or results
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotPerformance = function(obj, ...)
{
   UseMethod("plotPerformance")   
}  

#' Predictions
#' 
#' @details
#' Generic function for showing predicted values for classification or regression model or results
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
showPredictions = function(obj, ...)
{
   UseMethod("showPredictions")   
}  

#' X residuals plot
#' 
#' @details
#' Generic function for plotting x residuals for classification or regression model or results
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotXResiduals = function(obj, ...)
{   
   UseMethod("plotXResiduals")
}   

#' Y residuals plot
#' 
#' @details
#' Generic function for plotting y residuals for classification or regression model or results
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotYResiduals = function(obj, ...)
{   
   UseMethod("plotYResiduals")
}   

#' X variance plot
#' 
#' @details
#' Generic function for plotting explained variance for decomposition of x data
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotXVariance = function(obj, ...)
{   
   UseMethod("plotXVariance")
}   

#' Y variance plot
#' 
#' @details
#' Generic function for plotting explained variance for decomposition of y data
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotYVariance = function(obj, ...)
{   
   UseMethod("plotYVariance")
}   

#' Biplot
#' 
#' @details
#' Generic function for biplot
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotBiplot = function(obj, ...)
{   
   UseMethod("plotBiplot")
}   

#' Scores plot
#' 
#' @details
#' Generic function for scores values for data decomposition
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotScores = function(obj, ...)
{   
   UseMethod("plotScores")
}   

#' X scores plot
#' 
#' @details
#' Generic function for plotting scores values for decomposition of x data
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotXScores = function(obj, ...)
{   
   UseMethod("plotXScores")
}   

#' XY scores plot
#' 
#' @details
#' Generic function for plotting scores values for decomposition of x and y data
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotXYScores = function(obj, ...)
{   
   UseMethod("plotXYScores")
}   

#' Selected intervals plot
#' 
#' @details
#' Generic function for plotting selected intervals or variables
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotSelection = function(obj, ...)
{   
   UseMethod("plotSelection")
}   

#' RMSE plot
#' 
#' @details
#' Generic function for plotting RMSE values vs. complexity of a regression model
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#'
#' @export
plotRMSE = function(obj, ...)
{   
   UseMethod("plotRMSE")
}   

#' Variance plot
#' 
#' @details
#' Generic function for plotting explained variance for data decomposition 
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotCumVariance = function(obj, ...)
{   
   UseMethod("plotCumVariance")
}   

#' X cumulative variance plot
#' 
#' @details
#' Generic function for plotting cumulative explained variance for decomposition of x data
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotXCumVariance = function(obj, ...)
{   
   UseMethod("plotXCumVariance")
}   

#' Y cumulative variance plot
#' 
#' @details
#' Generic function for plotting cumulative explained variance for decomposition of y data
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotYCumVariance = function(obj, ...)
{   
   UseMethod("plotYCumVariance")
}   

#' Loadings plot
#' 
#' @details
#' Generic function for plotting loadings values for data decomposition
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotLoadings = function(obj, ...)
{   
   UseMethod("plotLoadings")
}   

#' Predictions plot
#' 
#' @details
#' Generic function for plotting predicted values for classification or regression model or results
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotPredictions = function(obj, ...)
{   
   UseMethod("plotPredictions")
}   

#' Regression coefficients plot
#' 
#' @details
#' Generic function for plotting regression coefficients values for a regression model
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotRegcoeffs = function(obj, ...)
{   
   UseMethod("plotRegcoeffs")
}   

#' Residuals plot
#' 
#' @details
#' Generic function for plotting residual values for data decomposition
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotResiduals = function(obj, ...)
{   
   UseMethod("plotResiduals")
}   

#' Variance plot
#' 
#' @details
#' Generic function for plotting explained variance for data decomposition
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotVariance = function(obj, ...)
{   
   UseMethod("plotVariance")
}   

#' X loadings plot
#' 
#' @details
#' Generic function for plotting loadings values for decomposition of x data
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotXLoadings = function(obj, ...)
{   
   UseMethod("plotXLoadings")
}   

#' X loadings plot
#' 
#' @details
#' Generic function for plotting loadings values for decomposition of x and y data
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotXYLoadings = function(obj, ...)
{   
   UseMethod("plotXYLoadings")
}   

#' Statistic histogram 
#' 
#' @details
#' Generic function for plotting statistic histogram plot
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotHist = function(obj, ...)
{   
   UseMethod("plotHist")
}   

#' Correlation plot 
#' 
#' @details
#' Generic function for correlation plot
#' 
#' @param obj
#' a model or result object
#' @param ...
#' other arguments
#' 
#' @export
plotCorr = function(obj, ...)
{   
   UseMethod("plotCorr")
}   

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mdatools documentation built on July 7, 2018, 1 a.m.