Man pages for FRESA.CAD
Feature Selection Algorithms for Computer Aided Diagnosis

backVarElimination.BinIDI/NRI-based backwards variable elimination
backVarElimination.ResNeRI-based backwards variable elimination
baggedModelGet the bagged model from a list of models
barPlotCiErrorBar plot with error bars
benchmarkingCompare performance of different model fitting/filtering...
BESSCV BeSS fit
bootstrapValidation.BinBootstrap validation of binary classification models
bootstrapValidation.ResBootstrap validation of regression models
bootstrapVarElimination.BinIDI/NRI-based backwards variable elimination with...
bootstrapVarElimination.ResNeRI-based backwards variable elimination with bootstrapping
BSWiMSBSWiMS model selection
CancerVarNamesData frame used in several examples of this package
ClustClassHybrid Hierarchical Modeling
clusterISODATACluster Clustering using the Isodata Approach
crossValidationFeatureSelection.BinIDI/NRI-based selection of a linear, logistic, or Cox...
crossValidationFeatureSelection.ResNeRI-based selection of a linear, logistic, or Cox...
CV_signatureCross-validated Signature
EmpiricalSurvDiffEstimate the LR value and its associated p-values
ensemblePredictThe median prediction from a list of models
featureAdjustmentAdjust each listed variable to the provided set of covariates
filteredFitA generic fit method with a filtered step for feature...
Filter_mRMRFRESA.CAD wrapper of mRMRe::mRMR.classic
FilterUnivariateUnivariate Filters
ForwardModel.BinIDI/NRI-based feature selection procedure for linear,...
ForwardModel.ResNeRI-based feature selection procedure for linear, logistic,...
FRESA.CAD-packageFeatuRE Selection Algorithms for Computer-Aided Diagnosis...
FRESA.ModelAutomated model selection
FRESAScaleData frame normalization
getKNNpredictionFromFormulaPredict classification using KNN
getSignatureReturns a CV signature template
getVar.BinAnalysis of the effect of each term of a binary...
getVar.ResAnalysis of the effect of each term of a linear regression...
GMVEBSWiMSHybrid Hierarchical Modeling with GMVE and BSWiMS
GMVEClusterSet Clustering using the Generalized Minimum Volume Ellipsoid...
HCLAS_KNN_CLASSLatent class based modeling of binary outcomes
heatMapsPlot a heat map of selected variables
improvedResidualsEstimate the significance of the reduction of predicted...
jaccardMatrixJaccard Index of two labeled sets
KNN_methodKNN Setup for KNN prediction
LASSO_MINGLMNET fit with feature selection"
listTopCorrelatedVariablesList the variables that are highly correlated with each other
LM_RIDGE_MINRidge Linear Models
modelFittingFit a model to the data
NAIVE_BAYESNaive Bayes Modeling
nearestCentroidClass Label Based on the Minimum Mahalanobis Distance
nearestneighborimputenearest neighbor NA imputation
plot.bootstrapValidation.BinPlot ROC curves of bootstrap results
plot.bootstrapValidation.ResPlot ROC curves of bootstrap results
plot.FRESABenchmarkPlot the results of the model selection benchmark
plotModels.ROCPlot test ROC curves of each cross-validation model
predict.bessPredicts 'BESS' models
predict.CLUSTER_CLASSPredicts 'ClustClass' outcome
predictForFresaLinear or probabilistic prediction
predict.FRESA_BOOSTPredicts BOOST_BSWiMS models
predict.FRESA_FILTERFITPredicts 'filteredFit' models
predict.FRESAKNNPredicts 'class::knn' models
predict.FRESA_LASSOPredicts GLMNET fitted objects
predict.FRESA_NAIVEBAYESPredicts 'NAIVE_BAYES' models
predict.FRESA_RIDGEPredicts 'LM_RIDGE_MIN' models
predict.FRESAsignaturePredicts 'CVsignature' models
predict.FRESA_SVMPredicts 'TUNED_SVM' models
predict.GMVEPredicts 'GMVECluster' clusters
predict.GMVE_BSWiMSPredicts 'GMVEBSWiMS' outcome
predictionStatsPrediction Evaluation
randomCVCross Validation of Prediction Models
rankInverseNormalDataFramerank-based inverse normal transformation of the data
reportEquivalentVariablesReport the set of variables that will perform an equivalent...
residualForFRESAReturn residuals from prediction
signatureDistanceDistance to the signature template
summary.bootstrapValidationGenerate a report of the results obtained using the...
summary.fitFRESAReturns the summary of the fit
summaryReportReport the univariate analysis, the cross-validation analysis...
timeSeriesAnalysisFit the listed time series variables to a given model
trajectoriesPolyFeaturesExtract the per patient polynomial Coefficients of a feature...
TUNED_SVMTuned SVM
uniRankVarUnivariate analysis of features (additional values returned)
univariateRankVariablesUnivariate analysis of features
updateModel.BinUpdate the IDI/NRI-based model using new data or new...
updateModel.ResUpdate the NeRI-based model using new data or new threshold...
update.uniRankVarUpdate the univariate analysis using new data
FRESA.CAD documentation built on Jan. 13, 2021, 3:39 p.m.