DarioS/ClassifyR
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

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Functions
282
Source code
59
Man pages
33
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DarioS/ClassifyR: A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
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API

API for DarioS/ClassifyR
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

Global functions
.addIntermediates Source code
.addUserLevels Source code
.calcArea Source code
.calcPerformance Source code
.classifierKeywordToParams Source code
.densitiesCrossover Source code
.dlda Source code
.dmvnorm_diag Source code
.doSelection Source code
.doTest Source code
.doTrain Source code
.doTransform Source code
.filterCharacteristics Source code
.getFeaturesStrings Source code
.getNodeShape Source code
.methodFormals Source code
.permutations Source code
.posterior_probs Source code
.precisionPathwaysPredict Source code
.precisionPathwaysTrain Source code
.rebalanceTrainingClasses Source code
.selectionKeywordToFunction Source code
.transformKeywordToFunction Source code
.validationText Source code
CV Source code
ClassifyResult Man page
ClassifyResult,DataFrame,character,characterOrDataFrame-method Man page
ClassifyResult,DataFrame,character-method Man page
ClassifyResult-class Man page
CrossValParams Man page Source code
CrossValParams-class Man page
DLDAparams Source code
DLDApredictInterface Source code
DLDAtrainInterface Source code
DMDranking Source code
FeatureSetCollection Man page
FeatureSetCollection,list-method Man page
FeatureSetCollection-class Man page
GLMparams Source code
GLMpredictInterface Source code
GLMtrainInterface Source code
HuRI Man page
KolmogorovSmirnovRanking Source code
KullbackLeiblerRanking Source code
LASSOGLMparams Source code
METABRICclinical Man page
ModellingParams Man page Source code
ModellingParams-class Man page
NSCfeatures Source code
NSCparams Source code
NSCpredictInterface Source code
NSCtrainInterface Source code
PCAfeatures Source code
PredictParams Man page
PredictParams,characterOrFunction-method Man page
PredictParams,missing-method Man page
PredictParams-class Man page
RFparams Source code
ROCplot Man page
ROCplot,ClassifyResult-method Man page
ROCplot,list-method Man page
RSFparams Source code
SVMparams Source code
SVMpredictInterface Source code
SVMtrainInterface Source code
SelectParams Man page
SelectParams,characterOrList-method Man page
SelectParams,missing-method Man page
SelectParams-class Man page
TrainParams Man page
TrainParams,characterOrFunction-method Man page
TrainParams,missing-method Man page
TrainParams-class Man page
TransformParams Man page
TransformParams,ANY-method Man page
TransformParams,character-method Man page
TransformParams-class Man page
XGBfeatures Source code
XGBparams Source code
[,FeatureSetCollection,numeric,missing,ANY-method Man page
[[,FeatureSetCollection,ANY,missing-method Man page
actualOutcome Man page
actualOutcome,ClassifyResult-method Man page
allFeatureNames Man page
allFeatureNames,ClassifyResult-method Man page
asthma Man page
available Man page Source code
bartlettRanking Source code
bubblePlot Man page
bubblePlot.PrecisionPathways Man page Source code
calcCVperformance Man page Source code
calcCVperformance,ClassifyResult-method Man page
calcCostsAndPerformance Man page Source code
calcExternalPerformance Man page
calcExternalPerformance,Surv,numeric-method Man page
calcExternalPerformance,factor,factor-method Man page
calcExternalPerformance,factor,tabular-method Man page
calcPerformance Man page
chosenFeatureNames Man page
chosenFeatureNames,ClassifyResult-method Man page
classes Man page
classifyInterface Source code
cleanClassifier Source code
cleanNFeatures Source code
cleanSelectionMethod Source code
clinical Man page
colCoxTests Man page Source code
coxmatC Source code
coxnetParams Source code
coxnetPredictInterface Source code
coxnetTrainInterface Source code
coxphParams Source code
coxphPredictInterface Source code
coxphRanking Source code
coxphTrainInterface Source code
crissCrossPlot Man page Source code
crissCrossValidate Man page Source code
crossValidate Man page
crossValidate,DataFrame-method Man page
crossValidate,MultiAssayExperiment-method, Man page
crossValidate,MultiAssayExperimentOrList-method Man page
crossValidate,data.frame-method Man page
crossValidate,matrix-method Man page
differentMeansRanking Source code
distribution Man page
distribution,ClassifyResult-method Man page
easyHard Man page
easyHard,MultiAssayExperimentOrList-method Man page
edgeRranking Source code
edgesToHubNetworks Man page Source code
elasticNetGLMparams Source code
extractPrevalidation Source code
extremeGradientBoostingPredictInterface Source code
extremeGradientBoostingTrainInterface Source code
fastCox Source code
featureSetSummary Man page
featureSetSummary,DataFrame-method Man page
featureSetSummary,MultiAssayExperiment-method Man page
featureSetSummary,matrix-method Man page
features Man page
features,ClassifyResult-method Man page
finalModel Man page
finalModel,ClassifyResult-method Man page
fisherDiscriminant Source code
flowchart Man page
flowchart.PrecisionPathways Man page Source code
forestFeatures Source code
generateCrossValParams Source code
generateModellingParams Source code
generateMultiviewParams Source code
getLocationsAndScales Source code
interactorDifferences Man page
interactorDifferences,DataFrame-method Man page
interactorDifferences,MultiAssayExperiment-method Man page
interactorDifferences,matrix-method Man page
interactors Man page
kNNinterface Source code
kNNparams Source code
kTSPclassifier Source code
length,FeatureSetCollection-method Man page
leveneRanking Source code
likelihoodRatioRanking Source code
limmaRanking Source code
measurements Man page
mergeTrainInterface Source code
mixModelsParams Source code
mixModelsPredict Source code
mixModelsTrain Source code
models Man page
models,ClassifyResult-method Man page
naiveBayesKernel Source code
naiveBayesParams Source code
pairsDifferencesRanking Source code
pcaPredictInterface Source code
pcaTrainInterface Source code
penalisedFeatures Source code
penalisedGLMpredictInterface Source code
penalisedGLMtrainInterface Source code
performance Man page
performance,ClassifyResult-method Man page
performancePlot Man page
performancePlot,ClassifyResult-method Man page
performancePlot,list-method Man page
performanceTable Man page Source code
plotFeatureClasses Man page
plotFeatureClasses,DataFrame-method Man page
plotFeatureClasses,MultiAssayExperiment-method Man page
plotFeatureClasses,matrix-method Man page
precisionPathwaysPredict Man page
precisionPathwaysPredict,PrecisionPathways,MultiAssayExperimentO Man page
precisionPathwaysTrain Man page
precisionPathwaysTrain,MultiAssayExperimentOrList-method Man page
predict.dlda Source code
predict.trainedByClassifyR Man page Source code
predictions Man page
predictions,ClassifyResult-method Man page
prepareData Man page
prepareData,DataFrame-method Man page
prepareData,MultiAssayExperiment-method Man page
prepareData,data.frame-method Man page
prepareData,list-method Man page
prepareData,matrix-method Man page
prevalFeatures Source code
prevalPredictInterface Source code
prevalTrainInterface Source code
previousSelection Source code
previousTrained Source code
print.PrecisionPathways Source code
randomForestPredictInterface Source code
randomForestTrainInterface Source code
randomSelection Source code
rankingPlot Man page
rankingPlot,ClassifyResult-method Man page
rankingPlot,list-method Man page
rfsrcFeatures Source code
rfsrcPredictInterface Source code
rfsrcTrainInterface Source code
ridgeGLMparams Source code
runTest Man page
runTest,DataFrame-method Man page
runTest,MultiAssayExperiment-method Man page
runTest,matrix-method Man page
runTests Man page
runTests,DataFrame-method Man page
runTests,MultiAssayExperiment-method Man page
runTests,matrix-method Man page
sampleNames Man page
sampleNames,ClassifyResult-method Man page
samplesMetricMap Man page
samplesMetricMap,ClassifyResult-method Man page
samplesMetricMap,list-method Man page
samplesMetricMap,matrix-method Man page
samplesSplits Man page Source code
samplesSplits,CrossValParams-method Man page
samplesSplits,numeric-method Man page
selectMulti Source code
selectionPlot Man page
selectionPlot,ClassifyResult-method Man page
selectionPlot,list-method Man page
show,ClassifyResult-method Man page
show,FeatureSetCollection-method Man page
show,PredictParams-method Man page
show,SelectParams-method Man page
show,TrainParams-method Man page
show,TransformParams-method Man page
simplifyResults Source code
splitsTestInfo Man page Source code
strataPlot Man page
strataPlot.PrecisionPathways Man page Source code
subtractFromLocation Source code
summary.PrecisionPathways Man page Source code
totalPredictions Man page
totalPredictions,ClassifyResult-method Man page
train.DataFrame Man page Source code
train.MultiAssayExperiment Man page Source code
train.data.frame Man page Source code
train.list Man page Source code
train.matrix Man page Source code
tunedParameters Man page
tunedParameters,ClassifyResult-method Man page
DarioS/ClassifyR documentation built on Dec. 19, 2024, 8:22 p.m.

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