| Assess Covariate Balance | assess_balance |
| Build Survival Analysis Dataset | build_survival_dataset |
| Calculate air pollution exposure averages | calculate_air_pollution |
| Calculate blood pressure from multiple readings | calculate_blood_pressure |
| Calculate diet score | calculate_diet_score |
| Calculate IPTW Weights | calculate_weights |
| Classify UK Biobank metabolite names | classify_metabolites |
| Extract Coefficients from Mediation Results | coef.mediation_result |
| Combine Multiple Disease Definitions | combine_disease_definitions |
| Compare Case Counts Across Data Sources | compare_data_sources |
| Compute topological metrics for a PPI network | compute_protein_ppi_metrics |
| Confidence Intervals for Mediation Results | confint.mediation_result |
| Create a baseline table comparing cases and controls under different conditions. | create_baseline_table |
| Create Disease Definition Object | create_disease_definition |
| Create an imputationList Object | create_imputation_list |
| Create a medication definition object | create_medication_definition |
| Estimate Propensity Score | estimate_propensity_score |
| Extract Cases by Specified Data Sources | extract_cases_by_source |
| Extract Baseline Diabetes Subtypes (T1DM/T2DM) with HbA1c Support | extract_diabetes_subtype_baseline |
| Extract participant-level disease diagnosis status | extract_disease_diagnosis |
| Extract Disease History (Prevalent Cases) for Covariates | extract_disease_history |
| Extract Disease History with Multiple Source Comparisons | extract_disease_history_sensitivity |
| Extract medication use from UKB drug fields | extract_medications |
| Extract self-reported medication indicators from field 20003 | extract_self_report_medications |
| Fit Regression Models on Multiple Imputed Datasets | fit_mi_models |
| Extract Death Dates for All Deceased Participants | get_death_dates |
| Query the built-in disease code catalog | get_disease_catalog |
| Get one UK Biobank field's metadata | get_field_info |
| Get structured UK Biobank field metadata | get_field_metadata |
| Query the built-in medication code catalog | get_medication_catalog |
| Get Pomegranate-derived disease definitions | get_pomegranate_diseases |
| Get the Pomegranate source manifest | get_pomegranate_source_manifest |
| Get Predefined Disease Definitions | get_predefined_diseases |
| Get predefined UK Biobank medication definitions | get_predefined_medications |
| Retrieve a STRING PPI network for proteomics hits | get_protein_ppi |
| Get column names of the synthetic UK Biobank-style demo dataset | get_ukb_demo_colnames |
| Get information about available variables | get_variable_info |
| Get one curated UK Biobank variable set | get_variable_set |
| Curated UK Biobank variable sets for extraction | get_variable_sets |
| Load the Pomegranate portal coding evidence table | load_pomegranate_portal_coding |
| Load UK Biobank field 20003 medication coding | load_ukb_medication_coding |
| Load the bundled UK Biobank non-ratio metabolite panel | load_ukb_metabolite_panel |
| Propensity Score Matching | match_propensity |
| Map metabolite names to MetaboAnalyst-compatible names | metabolite_to_metaboanalyst_name |
| Parse Cancer Registry Records | parse_cancer_registry |
| Parse Death Registry Records | parse_death_records |
| Parse ICD-10 Hospital Diagnosis Records | parse_icd10_diagnoses |
| Parse ICD-9 Hospital Diagnosis Records | parse_icd9_diagnoses |
| Parse OPCS4 Hospital Procedure Records | parse_opcs4_procedures |
| Parse Self-Reported Illness Records | parse_self_reported_illnesses |
| Plot Covariate Balance (Love Plot) | plot_balance |
| Plot Calibration Curve | plot_calibration |
| Visualize correlation matrix as a heatmap | plot_correlation |
| Plot training-validation Cox log(HR) concordance | plot_cox_loghr_correlation |
| Plot sensitivity-analysis Cox log(HR) concordance | plot_cox_sensitivity_correlation |
| Plot enrichment results as a lollipop chart via TCMDATA | plot_enrichment_lollipop |
| Plot Forest Plot for Subgroup Analysis | plot_forest |
| Plot GO ORA results as a bar chart via TCMDATA | plot_go_ora_bar |
| Plot a publication-style heatmap | plot_heatmap |
| Plot Kaplan-Meier Survival Curve | plot_km_curve |
| Plot Mediation Analysis Results | plot_mediation |
| Plot Forest Plot for Multiple Mediator Analysis | plot_mediation_forest |
| Plot metabolite ORA results as a bar plot | plot_metabolite_ora_barplot |
| Plot metabolite ORA results as a dot plot | plot_metabolite_ora_dotplot |
| Plot Multiple Imputation Diagnostics | plot_mi_diagnostics |
| Plot Multiple Imputation Pooled Results | plot_mi_pooled |
| Plot Calibration Curve | plot_ml_calibration |
| Plot Model Comparison | plot_ml_compare |
| Plot Confusion Matrix | plot_ml_confusion |
| Plot Decision Curve Analysis | plot_ml_dca |
| Plot Gain Curve | plot_ml_gain |
| Plot Variable Importance | plot_ml_importance |
| Plot KS Curve | plot_ml_ks |
| Plot Lift Curve | plot_ml_lift |
| Plot PR Curve | plot_ml_pr |
| Plot ROC Curves | plot_ml_roc |
| Plot One or More ROC Curves from Tidy ROC Data | plot_ml_roc_compare |
| Plot a participant flow table | plot_participant_flow |
| Plot Propensity Score Distribution | plot_ps_distribution |
| Plot a restricted cubic spline exposure-response curve | plot.ukb_rcs plot_rcs plot_rcs.ukb_rcs |
| Plot a volcano-style regression summary | plot_regression_volcano |
| Plot a publication-style scatter plot | plot_scatter |
| Plot SHAP Beeswarm Summary | plot_shap_beeswarm |
| Plot SHAP Dependence | plot_shap_dependence |
| Plot SHAP Force (Waterfall) | plot_shap_force |
| Plot SHAP Summary | plot_shap_summary |
| Plot a publication-style stacked bar chart | plot_stacked_bar |
| Plot top positive and inverse Cox associations | plot_top_hr_bars |
| Plot a publication-style violin plot | plot_violin |
| Plot a UKB ML Flow Object | plot.ukb_ml_flow |
| Plot a UKB ML Flow Comparison Object | plot.ukb_ml_flow_compare |
| Pool Custom Estimates from Multiple Imputations | pool_custom_estimates |
| Pool Results from Multiple Imputation Models | pool_mi_models |
| Preprocess UKB baseline variables | preprocess_baseline |
| Print Method for Mediation Results | print.mediation_result |
| Convert protein identifiers to gene symbols | protein_to_gene_symbol |
| Rank nodes in a PPI network by integrated centrality | rank_protein_ppi_nodes |
| Extract RAP Phenotype Data Synchronously | rap_extract_pheno |
| Find the RAP Dataset File in the Current Project | rap_find_dataset |
| List Approved RAP Dataset Fields | rap_list_fields |
| Plan a RAP Phenotype Extraction | rap_plan_extract |
| Submit a RAP Table-Exporter Phenotype Extraction Job | rap_submit_extract |
| Calculate correlation between variables | run_correlation |
| Multiple imputation and merge back to full data | run_imputation |
| Run Causal Mediation Analysis | run_mediation |
| Run metabolite over-representation analysis | run_metabolite_ora |
| Run Multiple Mediator Analysis | run_multi_mediator |
| Run Multiple Subgroup Analyses | run_multi_subgroup |
| Run KEGG ORA enrichment for proteomics hits | run_protein_kegg_ora |
| Run GO ORA enrichment for proteomics hits | run_protein_ora |
| Cluster a protein-protein interaction network | run_protein_ppi_clustering |
| Evaluate PPI network robustness for selected protein targets | run_protein_ppi_robustness |
| Fit a restricted cubic spline exposure-response model | run_rcs |
| Run a regression model (unified interface) | run_regression |
| Sensitivity Analysis for Mediation | run_sensitivity_mediation |
| Run Subgroup Analysis | run_subgroup_analysis |
| Run Weighted Analysis | run_weighted_analysis |
| Run Multiple Fine-Gray Competing-Risk Models | runmulti_competing |
| Run multiple Cox proportional hazards models | runmulti_cox |
| Run Lagged Cox Sensitivity Analyses | runmulti_cox_lag |
| Run Multiple Cox Models with PH Diagnostics | runmulti_cox_zph |
| Run multiple generalised additive models | runmulti_gam |
| Run multiple generalised linear models | runmulti_glm |
| Run multiple linear regression models | runmulti_lm |
| Run multiple logistic regression models | runmulti_logit |
| Run multiple negative-binomial regression models | runmulti_negbin |
| Run Grouped-Exposure Trend Tests | runmulti_trend |
| Score network clusters in a PPI graph | score_protein_ppi_clusters |
| Select Incident Cases by Time Since Enrollment | select_incident_by_years |
| Exclude Early Events for Sensitivity Analysis | sensitivity_exclude_early_events |
| Exclude Rows with Missing Covariates for Sensitivity Analysis | sensitivity_exclude_missing_covariates |
| Filter a STRING PPI network via TCMDATA | subset_protein_ppi |
| Summary Method for Mediation Results | summary.mediation_result |
| Tidy Method for mi_pooled_result | tidy.mi_pooled_result |
| Check the UK Biobank RAP execution environment | ukb_check_rap_env |
| Clean UK Biobank Missing and Non-response Values | ukb_clean_missing |
| Compare Cox results between training and validation sets | ukb_compare_cox_results |
| Compare sensitivity Cox results against a main analysis | ukb_compare_sensitivity_cox |
| Diagnose Proportional Hazards Assumptions for a Cox Model | ukb_cox_diagnostics |
| Create a RAP extraction manifest | ukb_create_extraction_manifest |
| Decode UK Biobank RAP exports | ukb_decode |
| Decode UK Biobank column names | ukb_decode_column_names |
| Decode UK Biobank coded values | ukb_decode_values |
| Generate a small synthetic UK Biobank-style demo dataset | ukb_demo |
| Chinese UK Biobank field-path dictionary | ukb_dictionary_zh |
| Download the official RAP data dictionary | ukb_download_rap_dictionary |
| Extract UK Biobank fields from a search result or field list | ukb_extract_fields |
| Inspect one UK Biobank field | ukb_field_info |
| Set up UK Biobank metadata for search, extraction, and decoding | ukb_metadata_setup |
| Standardize Manual ML Train/Test Splits | ukb_ml_as_split |
| Calibration Curve Analysis | ukb_ml_calibration |
| Compare Multiple ML Models | ukb_ml_compare |
| Compare Multiple Feature Sets with a Frozen-Test ML Workflow | ukb_ml_compare_feature_sets |
| Compare Multiple Feature Sets and/or Models | ukb_ml_compare_flows |
| Confusion Matrix | ukb_ml_confusion |
| Cross-Validation for ML Models | ukb_ml_cv |
| Decision Curve Analysis | ukb_ml_dca |
| Evaluate the Final Model Once on the Frozen Test Set | ukb_ml_evaluate_test |
| Select Features for UKB ML Workflows | ukb_ml_feature_select |
| Refit the Final ML Model on Training Development Data | ukb_ml_fit_final |
| Run a Complete Single-Model UKB ML Flow | ukb_ml_flow |
| Gain and Lift Curve Analysis | ukb_ml_gain_lift |
| Get Variable Importance | ukb_ml_importance |
| KS Curve Analysis | ukb_ml_ks |
| Calculate Model Performance Metrics | ukb_ml_metrics |
| Train a Machine Learning Model | ukb_ml_model |
| Precision-Recall Curve Analysis | ukb_ml_pr |
| Predict from ML Model | ukb_ml_predict |
| ROC Curve Analysis | ukb_ml_roc |
| Create ROC Curve Data for Binary ML Predictions | ukb_ml_roc_data |
| Split Data into Frozen ML Train/Test Sets | ukb_ml_split_data |
| List Supported Machine Learning Models | ukb_ml_supported_models |
| Train Survival Machine Learning Model | ukb_ml_survival |
| Standardize Manual Survival ML Train/Test Splits | ukb_ml_survival_as_split |
| Evaluate Survival ML Once on the Frozen Test Set | ukb_ml_survival_evaluate_test |
| Select Features for Survival ML Workflows | ukb_ml_survival_feature_select |
| Refit Final Survival ML Model | ukb_ml_survival_fit_final |
| Get Variable Importance for Survival Model | ukb_ml_survival_importance |
| Predict from Survival ML Model | ukb_ml_survival_predict |
| SHAP Values for Survival Models | ukb_ml_survival_shap |
| Split Data into Frozen Survival ML Train/Test Sets | ukb_ml_survival_split_data |
| Tune Survival ML Hyperparameters Without Touching the Test Set | ukb_ml_survival_tune |
| Run a Frozen-Test Survival ML Workflow | ukb_ml_survival_workflow |
| Learn a Binary Classification Threshold | ukb_ml_threshold |
| Tune ML Hyperparameters Without Touching the Test Set | ukb_ml_tune |
| Run a Frozen-Test UKB ML Workflow | ukb_ml_workflow |
| Build a participant flow table | ukb_participant_flow |
| Annotate Olink-style protein variables | ukb_protein_annotation |
| Query UK Biobank dictionary metadata | ukb_query_dictionary |
| Standardize variables using existing scaling parameters | ukb_scale_with_parameters |
| Search UK Biobank fields | ukb_search_fields |
| Run a Cox sensitivity-analysis suite | ukb_sensitivity_suite |
| Compute SHAP Values | ukb_shap |
| SHAP Dependence Values | ukb_shap_dependence |
| SHAP Force Plot Data | ukb_shap_force |
| SHAP Summary Statistics | ukb_shap_summary |
| Record or Retrieve UKB Cohort Snapshots | ukb_snapshot |
| Standardize variables using training-set parameters | ukb_standardize_by_train |
| Build a UK Biobank follow-up time skeleton | ukb_time_skeleton |
| Select top Cox associations by hazard ratio | ukb_top_hr_results |
| Run Cox models in training and validation sets | ukb_train_validation_cox |
| Validate requested columns against a data object | ukb_validate_columns |
| Write a RAP extraction manifest | ukb_write_extraction_manifest |
| UKBAnalytica: UK Biobank Data Processing and Survival Analysis Toolkit | UKBAnalytica-package UKBAnalytica |
