# UK Biobank Data Processing and Survival Analysis Toolkit

## Documentation for package ‘UKBAnalytica’ version 1.0.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C E F G L M P R S T U

UKBAnalytica-package | UKBAnalytica: UK Biobank Data Processing and Survival Analysis Toolkit

## -- A --

assess_balance | Assess Covariate Balance

## -- B --

build_survival_dataset | Build Survival Analysis Dataset

## -- C --

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

## -- E --

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

## -- F --

fit_mi_models | Fit Regression Models on Multiple Imputed Datasets

## -- G --

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

## -- L --

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

## -- M --

match_propensity | Propensity Score Matching
metabolite_to_metaboanalyst_name | Map metabolite names to MetaboAnalyst-compatible names

## -- P --

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.ukb_rcs | Plot a restricted cubic spline exposure-response curve
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_rcs.ukb_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

## -- R --

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
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
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

## -- S --

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

## -- T --

tidy.mi_pooled_result | Tidy Method for mi_pooled_result

## -- U --

UKBAnalytica | UKBAnalytica: UK Biobank Data Processing and Survival Analysis Toolkit
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