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