FRESA.CAD (version 3.3.0)

randomCV: Cross Validation of Prediction Models

Description

The data set will be divided into a random train set and a test sets. The train set will be modeled by the user provided fitting method. Each fitting method must have a prediction function that will be used to predict the outcome of the test set.

Usage

randomCV(theData = NULL,
             theOutcome = "Class",
             fittingFunction=NULL, 
             trainFraction = 0.5,
             repetitions = 100,
             trainSampleSets=NULL,
             featureSelectionFunction=NULL,
             featureSelection.control=NULL,
             asFactor=FALSE,
             addNoise=FALSE,
             classSamplingType=c("Augmented","NoAugmented","Proportional","Balanced"),
             ...
             )

Arguments

theData

The data-frame for cross-validation

theOutcome

The name of the outcome

fittingFunction

The fitting function used to model the data

trainFraction

The percentage of the data to be used for training

repetitions

The number of times that the CV process will be repeated

trainSampleSets

A set of train samples

featureSelectionFunction

The feature selection function to be used to filter out irrelevant features

featureSelection.control

The parameters to control the feature selection function

asFactor

Set theOutcome as factor

addNoise

if TRUE will add 0.1

classSamplingType

if "Proportional": proportional to the data classes. "Augmented": Augment samples to balance training class "NoAugmented": Avoid Data augmentation hece training may not be balanced "Balanced": All class in training set have the same samples

...

Parameters to be passed to the fitting function

Value

testPredictions

All the predicted outcomes. Is a data matrix with three columns c("Outcome","Model","Prediction"). Each row has a prediction for a given test subject

trainPredictions

All the predicted outcomes in the train data set. Is a data matrix with three columns c("Outcome","Model","Prediction"). Each row has a prediction for a given test subject

medianTest

The median of the test prediction for each subject

medianTrain

The median of the prediction for each train subject

boxstaTest

The statistics of the boxplot for test data

boxstaTrain

The statistics of the boxplot for train data

trainSamplesSets

The id of the subjects used for training

selectedFeaturesSet

A list with all the features used at each training cycle

featureFrequency

A order table object that describes how many times a feature was selected.

jaccard

The jaccard index of the features as well as the average number of features used for prediction

theTimes

The CPU time analysis

Examples

# NOT RUN {
	
# }
# NOT RUN {
        ### Cross Validation Example ####
        # Start the graphics device driver to save all plots in a pdf format
        pdf(file = "CrossValidationExample.pdf",width = 8, height = 6)

        # Get the stage C prostate cancer data from the rpart package
        data(stagec,package = "rpart")

        # Prepare the data. Create a model matrix with interactions but no event time 
        stagec$pgtime <- NULL
        stagec$eet <- as.factor(stagec$eet)
        options(na.action = 'na.pass')
        stagec_mat <- cbind(pgstat = stagec$pgstat,
                         as.data.frame(model.matrix(pgstat ~ .*.,stagec))[-1])
        fnames <- colnames(stagec_mat)
        fnames <- str_replace_all(fnames,":","__")
        colnames(stagec_mat) <- fnames

        # Impute the missing data
        dataCancerImputed <- nearestNeighborImpute(stagec_mat)
        dataCancerImputed[,1:ncol(dataCancerImputed)] <- sapply(dataCancerImputed,as.numeric)

        # Cross validating a Random Forest classifier
        cvRF <- randomCV(dataCancerImputed,"pgstat",
                         randomForest::randomForest,
                         trainFraction = 0.8, 
                         repetitions = 10,
                         asFactor = TRUE);

        # Evaluate the prediction performance of the Random Forest classifier
        RFStats <- predictionStats_binary(cvRF$medianTest,
        plotname = "Random Forest",cex = 0.9);

        # Cross validating a BSWiMS with the same train/test set
        cvBSWiMS <- randomCV(fittingFunction = BSWiMS.model,
        	trainSampleSets = cvRF$trainSamplesSets);

        # Evaluate the prediction performance of the BSWiMS classifier
        BSWiMSStats <- predictionStats_binary(cvBSWiMS$medianTest,
        	plotname = "BSWiMS",cex = 0.9);

        # Cross validating a LDA classifier with a t-student filter
        cvLDA <- randomCV(dataCancerImputed,"pgstat",MASS::lda,
                          trainSampleSets = cvRF$trainSamplesSets,
                          featureSelectionFunction = univariate_tstudent,
                          featureSelection.control = list(limit = 0.5,thr = 0.975));

        # Evaluate the prediction performance of the LDA classifier
        LDAStats <- predictionStats_binary(cvLDA$medianTest,plotname = "LDA",cex = 0.9);

        # Cross validating a QDA classifier with LDA t-student features and RF train/test set
        cvQDA <- randomCV(fittingFunction = MASS::qda,
                          trainSampleSets = cvRF$trainSamplesSets,
                          featureSelectionFunction = cvLDA$selectedFeaturesSet);

        # Evaluate the prediction performance of the QDA classifier
        QDAStats <- predictionStats_binary(cvQDA$medianTest,plotname = "QDA",cex = 0.9);

        #Create a barplot with 95<!-- %CI that compare the balance error of the classifiers -->
        errorciTable <- rbind(RFStats$berror,
        	BSWiMSStats$berror,
        	LDAStats$berror,
        	QDAStats$berror)

        bpCI <- barPlotCiError(as.matrix(errorciTable),metricname = "Balanced Error",
                        	   thesets =  c("Classifier Method"),
                        	   themethod = c("RF","BSWiMS","LDA","QDA"),
                        	   main = "Balanced Error",
                        	   offsets = c(0.5,0.15),
                        	   scoreDirection = "<",
                        	   ho = 0.5,
                        	   args.legend = list(bg = "white",x = "topright"),
                        	   col = terrain.colors(4));



        dev.off()
	
# }