Files in familiar

End-to-End Automated Machine Learning and Model Evaluation

NEWS.md R/NoveltyDetectorS4NoneNoveltyDetector.R R/PlotUnivariateImportance.R R/HyperparameterS4BayesianAdditiveRegressionTrees.R R/FamiliarSharedS4Methods.R R/CombatNormalisation.R R/LearnerRecalibration.R R/PlotICE.R R/FamiliarHyperparameterLearner.R R/MetricS4Regression.R R/ClusterRepresentation.R R/Clustering.R R/HyperparameterOptimisationMetaLearners.R R/PairwiseSimilarity.R R/FamiliarDataComputationAUCCurves.R R/FunctionWrapperUtilities.R R/ProcessTimeUtilities.R R/BatchNormalisation.R R/LearnerS4RFSRC.R R/PlotFeatureSimilarity.R R/DataPreProcessing.R R/OutcomeInfo.R R/DataProcessing.R R/Imputation.R R/Logger.R R/VimpS4CoreLearn.R R/LearnerSurvivalGrouping.R R/LearnerS4Cox.R R/LearnerS4SurvivalRegression.R R/CheckPackages.R R/VimpS4Concordance.R R/PlotDecisionCurves.R R/ParseData.R R/FamiliarDataComputationICE.R R/FamiliarObjectConversion.R R/SocketServer.R R/FamiliarDataComputationModelPerformance.R R/FamiliarCollectionExport.R R/LearnerMain.R R/FamiliarS4Generics.R R/PlotColours.R R/PlotCalibration.R R/HyperparameterS4RandomSearch.R R/ExperimentSetup.R R/ParseSettings.R R/RandomGrouping.R R/FamiliarDataComputationCalibrationInfo.R R/TestDataCreators.R R/PlotModelPerformance.R R/FamiliarVimpMethod.R R/FamiliarObjectUpdate.R R/TrainS4Methods.R R/LearnerSurvivalProbability.R R/FamiliarDataComputationSampleSimilarity.R R/FamiliarEnsemble.R R/FamiliarNoveltyDetector.R R/PredictS4Methods.R R/BootstrapConfidenceInterval.R R/Familiar.R R/Normalisation.R R/PlotAll.R R/RankMain.R R/ClusteringMethod.R R/PlotGTable.R R/FamiliarData.R R/Utilities.R R/FamiliarModel.R R/CheckArguments.R R/LearnerS4NaiveBayes.R R/FamiliarDataComputationPredictionData.R R/LearnerS4Naive.R R/PlotConfusionMatrix.R R/VimpS4MutualInformation.R R/PlotSampleClustering.R R/FamiliarDataComputationFeatureSimilarity.R R/Transformation.R R/LearnerS4GLM.R R/UtilitiesS4.R R/ModelBuilding.R R/LearnerS4Ranger.R R/FamiliarDataComputationFeatureExpression.R R/ClassBalance.R R/RankSimpleAggregation.R R/FamiliarDataComputationHyperparameters.R R/HyperparameterOptimisation.R R/CheckHyperparameters.R R/ErrorMessages.R R/RankStabilityAggregation.R R/FamiliarDataComputationRiskStratificationInfo.R R/NoveltyDetectorS4IsolationTree.R R/MetricS4AUC.R R/PlotKaplanMeier.R R/Evaluation.R R/FamiliarDataComputationVimp.R R/LearnerS4KNN.R R/DataServerBackend.R R/LearnerS4MBoost.R R/FamiliarDataComputationDecisionCurveAnalysis.R R/NoveltyDetectorMain.R R/HyperparameterOptimisationUtilities.R R/FeatureSelection.R R/ExperimentData.R R/FamiliarDataComputationCalibrationData.R R/StringUtilities.R R/PlotInputArguments.R R/FamiliarDataElement.R R/MetricS4.R R/LearnerS4SVM.R R/PlotPermutationVariableImportance.R R/TestFunctions.R R/LearnerS4GLMnet.R R/FeatureInfo.R R/MetricS4ConcordanceIndex.R R/TrimUtilities.R R/HyperparameterS4GaussianProcess.R R/FamiliarDataComputationUnivariateAnalysis.R R/FeatureInfoParameters.R R/FamiliarDataComputation.R R/DataParameterChecks.R R/HyperparameterS4Ranger.R R/RankBordaAggregation.R R/Random.R R/VimpMain.R R/MetricS4ConfusionMatrixMetrics.R R/FamiliarDataComputationRiskStratificationData.R R/VimpS4Correlation.R R/FamiliarDataComputationPermutationVimp.R R/ParallelFunctions.R R/FamiliarS4Classes.R R/FamiliarCollection.R R/aaa.R R/PlotUtilities.R R/VimpTable.R R/FamiliarDataComputationConfusionMatrix.R R/MetricS4Brier.R R/VimpS4OtherMethods.R R/VimpS4Regression.R R/LearnerS4XGBoost.R R/PlotAUCcurves.R R/PlotFeatureRanking.R R/Iterations.R R/DataObject.R inst/doc/prospective_use_precompiled.Rmd inst/doc/learners_precompiled.Rmd inst/doc/feature_selection_precompiled.Rmd inst/doc/introduction_precompiled.Rmd inst/doc/performance_metrics_precompiled.Rmd inst/doc/evaluation_and_explanation_precompiled.Rmd tests/testthat.R tests/testthat/test-learner_glmnet_S4.R tests/testthat/test-plot_model_performance.R tests/testthat/test-learner_ranger_s4.R tests/testthat/test-learner_mboost_lm_S4.R tests/testthat/test-export_sample_clustering.R tests/testthat/test-dynamic_model_loading.R tests/testthat/test-learner_cox_s4.R tests/testthat/test-parallel_backend.R tests/testthat/test-novelty_isolation_forest_S4.R tests/testthat/test-plot_univariate_importance.R tests/testthat/test-learner_rfsrc_s4.R tests/testthat/test-0_plot_sample_clustering_a.R tests/testthat/test-learner_naive_bayes_S4.R tests/testthat/test-learner_mboost_tree_S4.R tests/testthat/test-function_wrappers.R tests/testthat/test-export_calibration_info.R tests/testthat/test-metric_concordance_index_S4.R tests/testthat/test-transformation.R tests/testthat/test-update_object.R tests/testthat/test-vimp_regression_S4.R tests/testthat/test-plot_decision_curve.R tests/testthat/test-plot_feature_similarity.R tests/testthat/test-0_plot_calibration.R tests/testthat/test-rank_aggregation_methods.R tests/testthat/test-train_familiar.R tests/testthat/test-predict.R tests/testthat/test-0_vimp_rfsrc_S4.R tests/testthat/test-learner_svm_S4.R tests/testthat/test-metric_auc_roc_S4.R tests/testthat/test-plot_kaplan_meier_curve.R tests/testthat/test-export_hyperparameters.R tests/testthat/test-experiment_data.R tests/testthat/test-collection_labels.R tests/testthat/test-vimp_mutual_information_S4.R tests/testthat/test-learner_knn_S4.R tests/testthat/test-metric_regression_S4.R tests/testthat/test-stratification.R tests/testthat/test-sample_weights.R tests/testthat/test-plot_permutation_variable_importance.R tests/testthat/test-learner_xgboost_lm_S4.R tests/testthat/test-process_time.R tests/testthat/test-batch_normalisation.R tests/testthat/test-vimp_concordance_S4.R tests/testthat/test-0_preprocessing_clustering.R tests/testthat/test-plot_model_ranks.R tests/testthat/test-export_risk_stratification_info.R tests/testthat/test-export_ice.R tests/testthat/test-learner_xgboost_dart_S4.R tests/testthat/test-plot_confusion_matrix.R tests/testthat/test-hyperparameter_optimisation.R tests/testthat/test-metric_brier_S4.R tests/testthat/test-plot_auc_curves.R tests/testthat/test-0_plot_sample_clustering_b.R tests/testthat/test-general_normalisation.R tests/testthat/test-0_plot_ice_b.R tests/testthat/test-0_plot_ice_a.R tests/testthat/test-metric_confusion_matrix_metrics_S4.R tests/testthat/test-export_prediction_data.R tests/testthat/test-vimp_ranger_S4.R tests/testthat/test-object_conversion.R tests/testthat/test-imputation.R tests/testthat/test-learner_glm_S4.R tests/testthat/test-learner_xgboost_tree_S4.R tests/testthat/test-configuration_file.R tests/testthat/test-vimp_correlation_S4.R tests/testthat/test-vimp_table.R tests/testthat/test-learner_survival_regression_S4.R tests/testthat/test-apply.R tests/testthat/test-subsampling_functions.R tests/testthat/test-vimp_glmnet_S4.R tests/testthat/test-vimp_corelearn_S4.R tests/testthat/test-experimental_design.R tests/testthat/test-naive_model.R tests/testthat/test-familiar_data_creation.R tests/testthat/test-novelty_none_S4.R tests/testthat/test-as_data_object.R vignettes/prospective_use_precompiled.Rmd vignettes/learners_precompiled.Rmd vignettes/feature_selection_precompiled.Rmd vignettes/introduction_precompiled.Rmd vignettes/performance_metrics_precompiled.Rmd vignettes/evaluation_and_explanation_precompiled.Rmd man/featureInfo-class.Rd man/theme_familiar.Rd man/export_hyperparameters-methods.Rd man/export_feature_expressions-methods.Rd man/export_all-methods.Rd man/train_familiar.Rd man/extract_model_vimp.Rd man/dot-check_plot_splitting_variables.Rd man/extract_dispatcher-familiarEnsemble-familiarDataElement-method.Rd man/vimpTable-class.Rd man/outcomeInfo-class.Rd man/dot-parse_categorical_features.Rd man/dot-check_feature_availability.Rd man/plot_kaplan_meier-methods.Rd man/export_calibration_info-methods.Rd man/summary-methods.Rd man/is.encapsulated_path.Rd man/dot-check_survival_time_plausibility.Rd man/export_auc_data-methods.Rd man/dot-parse_feature_selection_settings.Rd man/familiarMetric-class.Rd man/dot-load_iterations.Rd man/plot_ice-methods.Rd man/dot-parse_experiment_settings.Rd man/as_familiar_data-methods.Rd man/extract_feature_expression.Rd man/waiver.Rd man/familiarData-class.Rd man/dot-update_experimental_design_settings.Rd man/get_vimp_table-methods.Rd man/get_feature_names-familiarCollection-method.Rd man/set_data_set_names-familiarCollection-method.Rd man/featureInfoParameters-class.Rd man/familiarDataElement-class.Rd man/dot-get_iteration_data.Rd man/extract_risk_stratification_info.Rd man/export_confusion_matrix_data-methods.Rd man/plot_variable_importance-methods.Rd man/extract_hyperparameters.Rd man/export_permutation_vimp-methods.Rd man/extract_univariate_analysis.Rd man/plot_feature_similarity-methods.Rd man/create_randomised_groups.Rd man/plot_confusion_matrix-methods.Rd man/export_univariate_analysis_data-methods.Rd man/aggregate_vimp_table-methods.Rd man/as_familiar_collection-methods.Rd man/export_partial_dependence_data-methods.Rd man/as_data_object-methods.Rd man/dot-check_input_plot_args.Rd man/extract_feature_similarity.Rd man/extract_risk_stratification_data.Rd man/extract_fs_vimp.Rd man/plot_univariate_importance-methods.Rd man/set_object_name-familiarData-method.Rd man/dataObject-class.Rd man/extract_calibration_data.Rd man/set_risk_group_names-familiarCollection-method.Rd man/coef-methods.Rd man/familiarEnsemble-class.Rd man/plot_decision_curve-methods.Rd man/get_class_names-familiarCollection-method.Rd man/extract_calibration_info.Rd man/set_feature_names-familiarCollection-method.Rd man/dot-parse_preprocessing_settings.Rd man/get_fs_method_names-familiarCollection-method.Rd man/export_model_vimp-methods.Rd man/precompute_feature_info.Rd man/export_sample_similarity-methods.Rd man/dot-plot_permutation_variable_importance.Rd man/dot-parse_evaluation_settings.Rd man/predict-methods.Rd man/export_ice_data-methods.Rd man/dot-get_default_sign_size.Rd man/plot_pd-methods.Rd man/set_learner_names-familiarCollection-method.Rd man/plot_auc_precision_recall_curve-methods.Rd man/plot_permutation_variable_importance-methods.Rd man/dot-check_outcome_type_plausibility.Rd man/get_risk_group_names-familiarCollection-method.Rd man/dot-check_input_identifier_column.Rd man/dot-parse_hyperparameter_optimisation_settings.Rd man/extract_ice.Rd man/set_class_names-familiarCollection-method.Rd man/dot-prepare_familiar_data_sets.Rd man/extract_sample_similarity.Rd man/set_object_name-familiarModel-method.Rd man/export_prediction_data-methods.Rd man/get_xml_config.Rd man/encapsulate_path.Rd man/export_risk_stratification_info-methods.Rd man/extract_predictions.Rd man/extract_permutation_vimp.Rd man/plot_sample_clustering-methods.Rd man/plot_model_performance-methods.Rd man/familiarModel-class.Rd man/familiarHyperparameterLearner-class.Rd man/extract_confusion_matrix.Rd man/dot-check_class_level_plausibility.Rd man/dot-plot_univariate_importance.Rd man/summon_familiar.Rd man/plot_calibration_data-methods.Rd man/dot-impute_outcome_type.Rd man/get_learner_names-familiarCollection-method.Rd man/familiarNoveltyDetector-class.Rd man/dot-parse_integer_features.Rd man/update_object-methods.Rd man/export_decision_curve_analysis_data-methods.Rd man/experimentData-class.Rd man/dot-update_initial_settings.Rd man/export_feature_similarity-methods.Rd man/vcov-methods.Rd man/extract_decision_curve_data.Rd man/plot_auc_roc_curve-methods.Rd man/extract_data.Rd man/dot-parse_general_settings.Rd man/dot-parse_model_development_settings.Rd man/export_calibration_data-methods.Rd man/dot-parse_setup_settings.Rd man/precompute_data_assignment.Rd man/precompute_vimp.Rd man/export_fs_vimp-methods.Rd man/dot-parse_file_paths.Rd man/extract_auc_data.Rd man/dot-parse_initial_settings.Rd man/extract_experimental_setup.Rd man/export_model_performance-methods.Rd man/set_object_name-familiarEnsemble-method.Rd man/familiarCollection-class.Rd man/update_model_dir_path-methods.Rd man/familiarVimpMethod-class.Rd man/is.waive.Rd man/get_data_set_names-familiarCollection-method.Rd man/extract_performance.Rd man/export_risk_stratification_data-methods.Rd man/set_fs_method_names-familiarCollection-method.Rd man/as_familiar_ensemble-methods.Rd man/familiar.Rd man/dot-finish_data_preparation.Rd