API for predomics/predomicspkg
Interpretable Prediction in Omics Data
| Global functions | |
|---|---|
| AnalyseStableModels_LOO | Man page Source code |
| LPO_best_models | Man page Source code |
| RRallW | Source code |
| RRkBest | Source code |
| RRkRand | Source code |
| addListOfModelsToModelCollection | Source code |
| addModelToModelCollection | Source code |
| analyze.terda | Source code |
| analyzeImportanceFeatures | Man page Source code |
| analyzeImportanceFeaturesFBM | Man page Source code |
| analyzePopulationFeatures | Man page Source code |
| bestModelFeatureStability | Man page Source code |
| bestModelStability | Man page Source code |
| buildAndSolveReducedLp | Source code |
| check.X_y_w | Source code |
| check.input | Source code |
| check.tX_y_w | Source code |
| cir_test | Man page |
| cir_train | Man page |
| classify | Source code |
| cleanPopulation | Man page Source code |
| collapse | Source code |
| compare.perf | Source code |
| compare.perf2dim | Source code |
| computeCardEnrichment | Man page Source code |
| computeCoeffSVMLin | Man page Source code |
| computeConfusionMatrix | Man page Source code |
| computeEffectSizes | Man page Source code |
| computeFeatureMetrics | Man page |
| computeIntercept | Man page Source code |
| confInterBinomial | Source code |
| convergence.test | Man page Source code |
| countEachFeatureApperance | Source code |
| counter | Man page |
| crossing | Man page Source code |
| crossing2 | Man page Source code |
| crossingIndividual_v1 | Man page Source code |
| crossingIndividual_v2 | Man page Source code |
| crossingIndividual_v3 | Man page Source code |
| delZero | Source code |
| denseVecToModel | Man page Source code |
| digest | Man page Source code |
| digestModelCollection | Man page Source code |
| disectModel | Man page Source code |
| error.rate | Source code |
| estimateCoefficientsIndividual | Man page Source code |
| estimateFeatureImportance | Man page Source code |
| evaluateAUC | Man page Source code |
| evaluateAccuracy | Man page Source code |
| evaluateAdditionnalMetrics | Man page Source code |
| evaluateFeatureImportanceInPopulation | Man page Source code |
| evaluateFit | Man page Source code |
| evaluateIntercept | Man page Source code |
| evaluateModel | Man page Source code |
| evaluateModelRegression | Man page Source code |
| evaluatePopulation | Man page Source code |
| evaluatePrevalence | Man page Source code |
| evaluateYhat | Man page Source code |
| evolve | Man page Source code |
| evolve1 | Man page Source code |
| evolve2m | Man page Source code |
| evolve3m | Man page Source code |
| extremum.type | Source code |
| f | Source code |
| filterFeaturesByPrevalence | Man page Source code |
| filterNoSignal | Man page Source code |
| filterfeaturesK | Man page Source code |
| find.best.k | Source code |
| findk | Man page Source code |
| fit | Man page Source code |
| generateAllCombinations | Man page Source code |
| generateAllSingleFeatureModel | Source code |
| generator_metal | Man page Source code |
| getAbundance | Source code |
| getAccuracyIndividual | Source code |
| getAccuracyPopulation | Source code |
| getConds | Source code |
| getFeaturePrevalence | Man page Source code |
| getFeatures2Keep | Source code |
| getFitIndividual | Man page Source code |
| getFitModel | Man page Source code |
| getFitModels | Man page Source code |
| getFitPopulation | Man page Source code |
| getGraph | Man page Source code |
| getGraph_features | Source code |
| getImportanceFeaturesFBMobjects | Man page Source code |
| getIndicesIndividual | Man page Source code |
| getIndicesPopulation | Man page Source code |
| getMaxMinPrevalenceModel | Man page Source code |
| getModelScore | Man page Source code |
| getNBestModels | Man page Source code |
| getSign | Man page Source code |
| getTheBestIndividual | Source code |
| get_IndividualToBeMutated | Man page Source code |
| get_Parents | Man page Source code |
| glmnetRR | Man page Source code |
| ibd | Man page |
| index2names | Man page Source code |
| individual | Man page Source code |
| individualGetDenseVec | Man page Source code |
| individual_vec_v1 | Man page Source code |
| individual_vec_v2 | Man page Source code |
| individual_vec_v3 | Man page Source code |
| is.wholenumber | Source code |
| isClf | Man page Source code |
| isExperiment | Man page Source code |
| isLearnerSota | Man page Source code |
| isModel | Man page Source code |
| isModelBTR | Man page Source code |
| isModelCollection | Man page Source code |
| isModelSota | Man page Source code |
| isModelSotaGLMNET | Man page Source code |
| isModelSotaRF | Man page Source code |
| isModelSotaSVM | Man page Source code |
| isModelTerda | Man page Source code |
| isPopulation | Man page Source code |
| isclose | Man page Source code |
| listOfDenseVecToListOfModels | Man page Source code |
| listOfDenseVecToModelCollection | Man page Source code |
| listOfModels2ModelCollection | Man page Source code |
| listOfModelsToDenseCoefMatrix | Man page Source code |
| listOfModelsToListOfDenseVec | Man page Source code |
| listOfModelsToListOfSparseVec | Man page Source code |
| listOfSparseVecToListOfModels | Man page Source code |
| loadPopulation | Man page Source code |
| loadResults | Man page Source code |
| make.counter | Man page Source code |
| makeFeatureAnnot | Man page Source code |
| makeFeatureModelPrevalenceNetworkCooccur | Man page Source code |
| makeFeatureModelPrevalenceNetworkMiic | Man page Source code |
| matrix.conf | Source code |
| meltScoreList | Source code |
| mergeMeltBestScoreCV | Man page Source code |
| mergeMeltImportanceCV | Man page Source code |
| mergeMeltScoreCV | Man page Source code |
| mergeMeltScoreEmpirical | Man page Source code |
| mergeResults | Man page Source code |
| metal | Man page Source code |
| metal_fit | Source code |
| modelCollectionToPopulation | Man page Source code |
| modelSampling | Man page Source code |
| modelToDenseVec | Man page Source code |
| multipleRR | Man page Source code |
| multipleRR_par | Man page Source code |
| multiplot | Man page Source code |
| mutate | Man page Source code |
| mutate2 | Man page Source code |
| mutator_v1 | Man page Source code |
| mutator_v2 | Man page Source code |
| myAssert | Man page Source code |
| myAssertNotNullNorNa | Man page Source code |
| myRRSkbest | Source code |
| names2index | Man page Source code |
| normModelCoeffs | Man page Source code |
| norr | Source code |
| obesity | Man page |
| plotAUC | Man page Source code |
| plotAUCg | Man page Source code |
| plotAbundanceByClass | Man page Source code |
| plotComparativeBestCV | Man page Source code |
| plotComparativeCV | Man page Source code |
| plotComparativeEmpiricalScore | Man page Source code |
| plotComparativeResults | Man page Source code |
| plotComparativeResultsBest | Man page Source code |
| plotFeatureModelCoeffs | Man page Source code |
| plotImportanceFeaturesFBMobjects | Man page Source code |
| plotMGSQuality | Man page |
| plotModel | Man page Source code |
| plotModelScore | Man page Source code |
| plotPopulation | Man page Source code |
| plotPrevalence | Man page Source code |
| plotScoreBarcode | Man page Source code |
| pop_better | Source code |
| population | Man page Source code |
| population2 | Man page Source code |
| populationDenseVec | Man page Source code |
| populationGet_X | Man page Source code |
| populationSet_X | Man page Source code |
| populationToDataFrame | Man page Source code |
| predictPopulation | Man page Source code |
| prevCond | Source code |
| printClassifier | Man page Source code |
| printExperiment | Man page Source code |
| printModel | Man page Source code |
| printModelCollection | Man page Source code |
| printPopulation | Man page Source code |
| printRFObject | Source code |
| printy | Man page Source code |
| quartileDispersion | Source code |
| rankFeatures | Man page Source code |
| resetTags | Man page Source code |
| runClassifier | Man page Source code |
| runCrossval | Man page Source code |
| runsolver | Source code |
| savePopulation | Man page Source code |
| saveResults | Man page Source code |
| scoreRatio | Man page Source code |
| select | Man page Source code |
| selectBestPopulation | Man page Source code |
| selectElite | Man page Source code |
| selectIndividualToKeep | Man page Source code |
| selectMixed | Man page Source code |
| selectTournoi | Man page Source code |
| selector_v1 | Man page Source code |
| selector_v2 | Man page Source code |
| sim_inter | Man page Source code |
| sim_intra | Man page Source code |
| sortPopulation | Man page Source code |
| sota.glmnet | Man page Source code |
| sota.rf | Man page Source code |
| sota.rf_fit | Source code |
| sota.svm | Man page Source code |
| sota.svm_fit | Source code |
| sparseVecToModel | Man page Source code |
| summarySE | Man page Source code |
| t2d | Man page |
| t2dw | Man page |
| tableBestModels | Man page Source code |
| tag_Couples | Man page Source code |
| tag_SelectElite | Man page Source code |
| tag_SelectRandom | Man page Source code |
| tag_ToBeMutated | Man page Source code |
| tag_select | Man page Source code |
| terBeam | Man page Source code |
| terBeam_fit | Source code |
| terDA.AUC | Source code |
| terDA.LR | Source code |
| terDA.mindist | Source code |
| terDA.rr | Source code |
| terda | Man page Source code |
| terda_fit | Source code |
| terga1 | Man page Source code |
| terga1_fit | Man page Source code |
| terga2 | Man page Source code |
| terga2_fit | Man page Source code |
| tree_func | Source code |
| updateModelIndex | Man page Source code |
| updateObjectIndex | Man page Source code |
