Files in predomics/predomicspkg

Interpretable Prediction in Omics Data

R/analyzeImportantFeaturesFBM.R R/data.R R/global.lib.R R/global.visu.R R/metal.R R/metal.lib.R R/minitools.R R/predomics.R R/sota.glmnet.R R/sota.rf.R R/sota.svm.R R/stability.lib.R R/terbeam.R R/terbeam.lib.R R/terda.R R/terda.lib.R R/terga1.R R/terga1.lib.R R/terga2.R R/terga2.lib.R README.md articles/Authors.R articles/Authors.Rmd articles/FAQs.R articles/FAQs.Rmd articles/Features.R articles/Features.Rmd articles/Installation.R articles/Installation.Rmd articles/Screenshots.R articles/Screenshots.Rmd articles/Technologies.R articles/Technologies.Rmd articles/Usage.R articles/Usage.Rmd data/code_make_files.R man/AnalyseStableModels_LOO.Rd man/LPO_best_models.Rd man/analyzeImportanceFeatures.Rd man/analyzeImportanceFeaturesFBM.Rd man/analyzePopulationFeatures.Rd man/bestModelFeatureStability.Rd man/bestModelStability.Rd man/cir_test.Rd man/cir_train.Rd man/cleanPopulation.Rd man/computeCardEnrichment.Rd man/computeCoeffSVMLin.Rd man/computeConfusionMatrix.Rd man/computeEffectSizes.Rd man/computeFeatureMetrics.Rd man/computeIntercept.Rd man/convergence.test.Rd man/counter.Rd man/crossing.Rd man/crossing2.Rd man/crossingIndividual_v1.Rd man/crossingIndividual_v2.Rd man/crossingIndividual_v3.Rd man/denseVecToModel.Rd man/digest.Rd man/digestModelCollection.Rd man/disectModel.Rd man/estimateCoefficientsIndividual.Rd man/estimateFeatureImportance.Rd man/evaluateAUC.Rd man/evaluateAccuracy.Rd man/evaluateAdditionnalMetrics.Rd man/evaluateFeatureImportanceInPopulation.Rd man/evaluateFit.Rd man/evaluateIntercept.Rd man/evaluateModel.Rd man/evaluateModelRegression.Rd man/evaluatePopulation.Rd man/evaluatePrevalence.Rd man/evaluateYhat.Rd man/evolve.Rd man/evolve1.Rd man/evolve2m.Rd man/evolve3m.Rd man/filterFeaturesByPrevalence.Rd man/filterNoSignal.Rd man/filterfeaturesK.Rd man/findk.Rd man/fit.Rd man/generateAllCombinations.Rd man/generator_metal.Rd man/getFeaturePrevalence.Rd man/getFitIndividual.Rd man/getFitModel.Rd man/getFitModels.Rd man/getFitPopulation.Rd man/getGraph.Rd man/getImportanceFeaturesFBMobjects.Rd man/getIndicesIndividual.Rd man/getIndicesPopulation.Rd man/getMaxMinPrevalenceModel.Rd man/getModelScore.Rd man/getNBestModels.Rd man/getSign.Rd man/get_IndividualToBeMutated.Rd man/get_Parents.Rd man/glmnetRR.Rd man/ibd.Rd man/index2names.Rd man/individual.Rd man/individualGetDenseVec.Rd man/individual_vec_v1.Rd man/individual_vec_v2.Rd man/individual_vec_v3.Rd man/isClf.Rd man/isExperiment.Rd man/isLearnerSota.Rd man/isModel.Rd man/isModelBTR.Rd man/isModelCollection.Rd man/isModelSota.Rd man/isModelSotaGLMNET.Rd man/isModelSotaRF.Rd man/isModelSotaSVM.Rd man/isModelTerda.Rd man/isPopulation.Rd man/isclose.Rd man/listOfDenseVecToListOfModels.Rd man/listOfDenseVecToModelCollection.Rd man/listOfModels2ModelCollection.Rd man/listOfModelsToDenseCoefMatrix.Rd man/listOfModelsToListOfDenseVec.Rd man/listOfModelsToListOfSparseVec.Rd man/listOfSparseVecToListOfModels.Rd man/loadPopulation.Rd man/loadResults.Rd man/make.counter.Rd man/makeFeatureAnnot.Rd man/makeFeatureModelPrevalenceNetworkCooccur.Rd man/makeFeatureModelPrevalenceNetworkMiic.Rd man/mergeMeltBestScoreCV.Rd man/mergeMeltImportanceCV.Rd man/mergeMeltScoreCV.Rd man/mergeMeltScoreEmpirical.Rd man/mergeResults.Rd man/metal.Rd man/modelCollectionToPopulation.Rd man/modelSampling.Rd man/modelToDenseVec.Rd man/multipleRR.Rd man/multipleRR_par.Rd man/multiplot.Rd man/mutate.Rd man/mutate2.Rd man/mutator_v1.Rd man/mutator_v2.Rd man/myAssert.Rd man/myAssertNotNullNorNa.Rd man/names2index.Rd man/normModelCoeffs.Rd man/obesity.Rd man/plotAUC.Rd man/plotAUCg.Rd man/plotAbundanceByClass.Rd man/plotComparativeBestCV.Rd man/plotComparativeCV.Rd man/plotComparativeEmpiricalScore.Rd man/plotComparativeResults.Rd man/plotComparativeResultsBest.Rd man/plotFeatureModelCoeffs.Rd man/plotImportanceFeaturesFBMobjects.Rd man/plotMGSQuality.Rd man/plotModel.Rd man/plotModelScore.Rd man/plotPopulation.Rd man/plotPrevalence.Rd man/plotScoreBarcode.Rd man/population.Rd man/population2.Rd man/populationDenseVec.Rd man/populationGet_X.Rd man/populationSet_X.Rd man/populationToDataFrame.Rd man/predictPopulation.Rd man/printClassifier.Rd man/printExperiment.Rd man/printModel.Rd man/printModelCollection.Rd man/printPopulation.Rd man/printy.Rd man/rankFeatures.Rd man/resetTags.Rd man/runClassifier.Rd man/runCrossval.Rd man/savePopulation.Rd man/saveResults.Rd man/scoreRatio.Rd man/select.Rd man/selectBestPopulation.Rd man/selectElite.Rd man/selectIndividualToKeep.Rd man/selectMixed.Rd man/selectTournoi.Rd man/selector_v1.Rd man/selector_v2.Rd man/sim_inter.Rd man/sim_intra.Rd man/sortPopulation.Rd man/sota.glmnet.Rd man/sota.rf.Rd man/sota.svm.Rd man/sparseVecToModel.Rd man/summarySE.Rd man/t2d.Rd man/t2dw.Rd man/tableBestModels.Rd man/tag_Couples.Rd man/tag_SelectElite.Rd man/tag_SelectRandom.Rd man/tag_ToBeMutated.Rd man/tag_select.Rd man/terBeam.Rd man/terda.Rd man/terga1.Rd man/terga1_fit.Rd man/terga2.Rd man/terga2_fit.Rd man/updateModelIndex.Rd man/updateObjectIndex.Rd tests/testthat.R tests/testthat/test_tutto.R vignettes/Authors.Rmd vignettes/FAQs.Rmd vignettes/Features.Rmd vignettes/Installation.Rmd vignettes/Screenshots.Rmd vignettes/Technologies.Rmd vignettes/Usage.Rmd vignettes_disabled/PredomicsPlotting.Rmd vignettes_disabled/vignette.Rmd