| Covariate set handed to forestsearch()/mrct_region_sims() for the paper's observed vs unobserved analysis cases. | analysis_covariates |
| Analyze subgroup for summary table (OPTIMIZED) | analyze_subgroup |
| Random-benchmark subgroup specification | benchmark_spec |
| Bootstrap Results for ForestSearch with Bias Correction | bootstrap_results |
| Bootstrap Ystar Count Matrix | bootstrap_ystar |
| Build Classification Rate Table from Simulation Results | build_classification_table |
| Build Cox Model Formula | build_cox_formula |
| Build Estimation Properties Table from Simulation Results | build_estimation_table |
| Calibrate Censoring Adjustment to Match DGM Reference Distribution | calibrate_cens_adjust |
| Calibrate GLM Interaction for a Target Subgroup Effect Size | calibrate_glm_interaction |
| Calibrate k_inter for Target Subgroup Hazard Ratio | calibrate_k_inter |
| Calibrate k_treat for Target Overall Hazard Ratio | calibrate_k_treat |
| Calibrate L_eff from Simulation Results | calibrate_L_eff |
| Diagnose Censoring Consistency Between DGM Source Data and Simulated Data | check_censoring_dgm |
| Collect Results from foreach with Error Handling | collect_results |
| Compare Detection Curves Across Sample Sizes | compare_detection_curves |
| Compare Subgroup Membership Across Two Analyses | compare_fs_subgroups |
| Compare Multiple Survival Regression Models | compare_multiple_survreg |
| Compare forestsearch Runs Across Selection-Rule Combinations | compare_selection_rules |
| Compare two extreme-subgroups simulation studies | compare_subgroup_sims |
| Compute Probability of Detecting True Subgroup | compute_detection_probability |
| Compute Detection Probability for GLM Outcomes | compute_detection_probability_glm |
| Compute and Attach CDE Values to a DGM Object | compute_dgm_cde |
| Compute Naive and Split-Derived 95% CIs for Pareto Frontier Members | compute_frontier_cis |
| Compute node metrics for a policy tree | compute_node_metrics |
| Wald confidence intervals for DINA coefficients. | confint.dina |
| Resampling approximation to the splitting consistency rate | consistency_resample |
| Validate the consistency approximation against literal splitting (Cox) | consistency_resample_compare |
| Count ID Occurrences in Bootstrap Sample | count_boot_id |
| Comprehensive Wrapper for Cox Spline Analysis with AHR and CDE Plotting | cox_ahr_cde_analysis |
| Fit Cox Model with Cubic Spline for Treatment Effect Heterogeneity | cox_cs_fit |
| Cox model summary for subgroup (OPTIMIZED) | cox_summary |
| Create Data Generating Mechanism for MRCT Simulations | create_dgm_for_mrct |
| Create Forest Plot Theme with Size Controls | create_forest_theme |
| Create GBSG-Based AFT Data Generating Mechanism | create_gbsg_dgm |
| Compute GLM Effect Estimate for a Single Subgroup | create_glm_row |
| Helper Functions for GRF Subgroup Analysis | create_grf_config |
| Create Enhanced Summary Table for Baseline Characteristics | create_summary_table |
| Compare Multiple CV Results | cv_compare_results |
| Create Metrics Tables for Cross-Validation Results | cv_metrics_tables |
| Cross-Validation Subgroup Match Summary | CV_sgs |
| Create Summary Tables from forestsearch_KfoldOut Results | cv_summary_tables |
| Create Compact CV Summary Text | cv_summary_text |
| Effective Information for Binary Outcomes (Logistic) | d_eff_binary |
| Effective Information for Continuous Outcomes (Gaussian) | d_eff_continuous |
| Effective Information for Count Outcomes (Poisson) | d_eff_count |
| Effective Information for Survival (Cox PH) | d_eff_survival |
| Estimate heterogeneous treatment effects via DINA (data-frame interface) | dina |
| Bagged DINA with IJ variance (data-frame interface) | dina_bagged |
| Estimate heterogeneous treatment effects via DINA | dina_fit |
| Bagged DINA with infinitesimal-jackknife variance | dina_fit_bagged |
| Extract DINA per-covariate Pareto frontiers as forestsearch cuts | dina_frontier |
| Identify a harm subgroup from a DINA fit via univariate threshold search | dina_subgroup |
| Selection-adjusted bootstrap CI for dina_subgroup() | dina_subgroup_bootstrap |
| Standard within-subgroup treatment-effect model for a DINA subgroup | dina_subgroup_refit |
| Dummy-code a data frame (numeric pass-through, factors expanded) | dummy_encode |
| Early Stopping Decision | early_stop_decision |
| Estimate Propensity Scores | estimate_propensity_scores |
| Evaluate a Comparison Expression Without eval(parse()) | evaluate_comparison |
| Evaluate Consistency (Two-Stage Algorithm) | evaluate_consistency_twostage |
| Cache and validate cut expressions efficiently | evaluate_cuts_once |
| Evaluate Subgroup Consistency (Single-Stage) | evaluate_subgroup_consistency |
| Expand a seed covariate frame to n_super rows via a Gaussian copula. | expand_covariates |
| Describe the Pareto-Frontier Selection in Words | explain_pareto_selection |
| Recover the GRF arguments used inside a forestsearch run | extract_grf_args |
| Tidy summary of selected subgroups across a comparison run | extract_selected_subgroups |
| Generate Figure Note for Quarto/RMarkdown | figure_note |
| Filter a vector by LASSO-selected variables | filter_by_lassokeep |
| Filter and merge arguments for function calls | filter_call_args |
| Find k_inter Value to Achieve Target Harm Subgroup Hazard Ratio | find_k_inter_for_target_hr |
| Find the split that leads to a specific leaf node (deprecated) | find_leaf_split |
| Find Minimum Sample Size for Target Detection Power | find_required_sample_size |
| Fit causal survival forest | fit_causal_forest |
| Fit Cox Models for Subgroups | fit_cox_models |
| Fit policy trees up to specified depth | fit_policy_trees |
| Recommended figure height for a forest panel | forest_height |
| ForestSearch: Exploratory Subgroup Identification | forestsearch |
| ForestSearch Bootstrap with doFuture Parallelization | forestsearch_bootstrap_dofuture |
| ForestSearch K-Fold Cross-Validation | forestsearch_Kfold |
| ForestSearch K-Fold Cross-Validation Output Summary | forestsearch_KfoldOut |
| ForestSearch Repeated K-Fold Cross-Validation | forestsearch_tenfold |
| Format Bootstrap Results Table with gt | format_bootstrap_table |
| Format Confidence Interval for Estimates | format_CI |
| Format ForestSearch Details Output for Beamer Two-Column Display | format_fs_details |
| Format Operating Characteristics Results as GT Table | format_oc_results |
| Approximate Procedure-Level False Positive Rate | fpr_approx |
| Direct Simulation-Based FPR Calibration at a Specific Threshold Pair | fpr_calibration |
| Transfer Corrected FPR Prediction to a Nearby Threshold Pair | fpr_calibration_transfer |
| Per-Subject Membership Matrix for Pareto Frontier Members | frontier_member_flags |
| Assert the exported selected-subgroup membership matches forestsearch's own | fs_assert_membership |
| Calibrated declaration threshold and family-wise size of the p-star screen | fs_declaration_calibration print.fs_declaration_calibration |
| Design-time feasibility of a DGM's planted region | fs_dgm_feasibility print.fs_dgm_feasibility |
| Sampling Scale of the Difference-in-Means Estimator | fs_dgm_scale |
| Materialize the maxeff candidate family as 0/1 membership columns | fs_export_maxeff_family |
| Report which stages of the candidate family are data-dependent | fs_family_report print.fs_family_report |
| Operating False-Discovery Rate of a Fitted ForestSearch Analysis | fs_fdr_report |
| Stem tag for a (subgroup_method, sg_focus) pair | fs_focus_tag |
| Identification structure across a sweep | fs_identification_summary |
| Identification-structure table | fs_identification_table |
| Convert Factor Code to Label | FS_labels |
| Operating-Characteristics Summary of a Multiplier-Resampling Payload | fs_mr_oc_summary |
| Enumerate the candidate family on a DGM's population frame | fs_oc_family_enumerate |
| Sweep the declaration thresholds on one draw set per trial size | fs_oc_grid |
| Invert the family declaration rate for a target | fs_oc_invert |
| Predicted operating characteristics of the search over a candidate family | fs_oc_predict |
| Bias-vs-coverage display (three panels) | fs_plot_bias_coverage |
| Covariate signatures of the realized rules | fs_rule_covariate_pairs |
| Estimator Standard Deviation at a Given Trial Size | fs_scale_se |
| Bias and coverage summary for one simulation cell | fs_sim_bias_coverage |
| Symmetric Square Root of a Covariance Matrix | fs_sym_root |
| Run Guo and He Algorithm 3 on a forestsearch maxeff fit | fs_to_guohe |
| Generate Synthetic Survival Data using AFT Model with Flexible Subgroups | generate_aft_dgm_flex |
| Generate Synthetic Data using Bootstrap with Perturbation | generate_bootstrap_synthetic |
| Generate Bootstrap Sample with Added Noise | generate_bootstrap_with_noise |
| Generate Detection Probability Curve | generate_detection_curve |
| Generate Synthetic GBSG Data using Generalized Bootstrap | generate_gbsg_bootstrap_general |
| Generate GLM-Based Data Generating Mechanism | generate_glm_dgm |
| Get all combinations of subgroup factors up to maxk | get_combinations_info |
| Get forced cut expressions for variables | get_conf_force |
| Get J-quantile cut expressions for variables | get_conf_force_jq |
| Get indicator vector for selected subgroup factors | get_covs_in |
| Fit Cox Model for Subgroup | get_Cox_sg |
| Generate Prediction Dataset with Subgroup Treatment Recommendation | get_dfpred |
| Bootstrap Confidence Interval and Bias Correction Results | get_dfRes |
| ForestSearch Data Preparation and Feature Selection | get_FSdata |
| Get L_eff at a Given Sample Size | get_leff |
| Fast Cox Model HR Estimation | get_split_hr_fast |
| Get subgroup membership vector | get_subgroup_membership |
| ggplot2 / patchwork forest plot | gg_forest |
| Fit GLM with Spline Treatment-Biomarker Interaction | glm_cs_fit print.glm_cs_fit |
| GLM Treatment-Effect Profile for Continuous Biomarker Interaction | glm_effect_profile |
| Evaluates the performance of GRF-identified subgroups, including hazard ratios, bias, and predictive values. This function is typically used in simulation studies to assess the performance of the GRF subgroup identification method. | grf.subg.eval |
| GRF Subgroup Identification for GLM Outcomes | grf.subg.harm.glm |
| GRF Subgroup Identification for Survival Data | grf.subg.harm.survival |
| Cross-validated choice of the shrinkage tuning parameter r | guohe_adaptive_r |
| De-biased inference for the best subgroup over a large enumerated family | guohe_algorithm3 |
| Format Hazard Ratio and Confidence Interval | hrCI_format |
| Build an aft_dgm_flex with synthetic regions and paper-style effect structure. | inject_mrct_structure |
| Generate Narrative Interpretation of Estimation Properties | interpret_estimation_table |
| Interpret and Diagnose Search Configuration | interpret_search_config |
| LASSO selection for Cox model | lasso_selection |
| Find the Most Recent .rds File Matching a Pattern | latest_rds |
| Load L_eff Calibration Results | load_leff_calibration |
| Make an Effect-Estimator Closure | make_effect_estimator |
| Build the logistic region model and draw Region on a population. | make_region_model |
| Multiplier-resampling (MR) estimates table (bootstrap-table format) | mr_estimates_table |
| MRCT Regional Subgroup Simulation | mrct_region_sims |
| Truth by region on the super-population: prevalence, x_pred shift, causal AHR / CDE, and a large-sample Cox HR on UNCENSORED potential outcomes. Compare HR_cox_PO with the censored-trial HR from sim_region_metrics(): a gap between them isolates the prognostic-shift / follow-up-truncation mechanism (the Feb-2026 deck) from covariate shift (AHR itself differing by region). | mrct_truth_by_region |
| Calculate n and percent | n_pcnt |
| Format Pareto Frontier of Candidate Subgroups | pareto_frontier_table |
| Plot Detection Probability Curve | plot_detection_curve |
| Three-Panel Effect-Distribution Violin from Simulation Results | plot_effect_distribution |
| Covariate involvement across the sweep | plot_fs_identification_involvement |
| Composition of the identified subgroup by structure | plot_fs_identification_structure |
| Selected-covariate-pair frequencies | plot_fs_rule_pairs |
| Plot Kaplan-Meier Survival Difference Bands for ForestSearch Subgroups | plot_km_band_forestsearch |
| Combined Pareto-Frontier Plot Across Configurations Sharing a Passing Set | plot_pareto_combined |
| Plot the Pareto Frontier of Candidate Subgroups | plot_pareto_frontier |
| True log-HR psi0(x) along x_pred with region histograms (paper Fig. 3 analogue) | plot_region_modifier |
| Plot Distribution of Identified Subgroups | plot_sg_distribution |
| Plot GLM Subgroup Outcomes | plot.fs_binary_plot plot_sg_glm_outcomes print.fs_binary_plot |
| Plot ForestSearch Subgroup Results | plot_sg_results |
| Plot Weighted Kaplan-Meier Curves for ForestSearch Subgroups | plot_sg_weighted_km |
| Plot Spline Treatment Effect Function | plot_spline_treatment_effect |
| Plot Subgroup Analysis Results | plot_subgroup_effects |
| Plot Subgroup Results Forest Plot | plot_subgroup_results_forestplot |
| Plot ForestSearch Results | plot.forestsearch |
| Plot Method for ForestSearch Forest Plot | plot.fs_forestplot |
| Plot Method for fs_sg_plot Objects | plot.fs_sg_plot |
| Forest plot of an extreme-subgroups summary | plot.subgroup_sims_summary |
| Predict Corrected Null FPR | predict_fpr_corrected |
| Predicted DINA values for new covariate data. | predict.dina |
| Prepare subgroup data for analysis | prepare_subgroup_data |
| Print detailed output for debugging | print_grf_details |
| Print method for cox_ahr_cde objects | print.cox_ahr_cde |
| Print a bagged DINA fit. | print.dina_bagged |
| Print a 'dina_subgroup' result. | print.dina_subgroup |
| Print a 'dina_subgroup_bootstrap' result. | print.dina_subgroup_bootstrap |
| Print a 'dina_subgroup_refit' result. | print.dina_subgroup_refit |
| Print Method for forestsearch Objects | print.forestsearch |
| Print Method for forestsearch_comparison | print.forestsearch_comparison |
| Print method for 'fpr_calibration' objects | print.fpr_calibration |
| Print Method for ForestSearch Bootstrap Results | print.fs_bootstrap |
| Print Method for fs_cv_summary Objects | print.fs_cv_summary |
| Print method for 'fs_dgm_scale' objects | print.fs_dgm_scale |
| Print method for 'fs_fdr_report' objects | print.fs_fdr_report |
| Print Method for ForestSearch Forest Theme | print.fs_forest_theme |
| Print Method for ForestSearch Forest Plot | print.fs_forestplot |
| Print Method for K-Fold CV Results | print.fs_kfold |
| Print method for 'fs_mr_oc' objects | print.fs_mr_oc |
| Print Method for fs_sg_plot Objects | print.fs_sg_plot |
| Print Method for Repeated K-Fold CV Results | print.fs_tenfold |
| Print Method for fs_weighted_km Objects | print.fs_weighted_km |
| Print Method for gbsg_dgm Objects | print.gbsg_dgm |
| Print method for 'glm_dgm' objects | print.glm_dgm |
| Print method for glm_effect_profile objects | print.glm_effect_profile |
| Print method for guohe_a3 objects | print.guohe_a3 |
| Print method for guohe_ar objects | print.guohe_ar |
| Print method for 'hte_test' objects | print.hte_test |
| Print method for 'leff_calibration' objects | print.leff_calibration |
| Print method for survreg_comparison objects | print.multi_survreg_comparison |
| Process forced cut expression for a variable | process_conf_force_expr |
| Quick Plot KM Bands from ForestSearch | quick_km_band_plot |
| Render ForestSearch Forest Plot | render_forestplot |
| Render Reference Simulation Table as gt | render_reference_table |
| Reset a Parallel Worker Pool | reset_workers |
| RMST calculation for subgroup | rmst_calculation |
| Run Null Calibration Simulation | run_null_calibration |
| Run One Simulation Replicate | run_simulation_analysis |
| Run Single Consistency Split | run_single_consistency_split |
| Run the extreme-subgroups simulation study | run_subgroup_sims |
| Save ForestSearch Forest Plot to File | save_forestplot |
| Save L_eff Calibration Results | save_leff_calibration |
| Select best subgroup based on criterion | select_best_subgroup |
| Sensitivity Analysis of Hazard Ratios to k_inter | sensitivity_analysis_k_inter |
| Set Up a GBSG-Based AFT Data Generating Mechanism | setup_gbsg_dgm |
| Set up parallel processing for subgroup consistency | setup_parallel_SGcons |
| Output Subgroup Consistency Results | sg_consistency_out |
| Subgroup summary table estimates | SG_tab_estimates |
| Enhanced Subgroup Summary Tables (gt output) | sg_tables |
| Adaptive Figure Height for a Subgroup-Distribution Plot | sgdist_fig_height |
| Violin/Boxplot Visualization of HR Estimates | SGplot_estimates |
| Region-consistency metrics on a simulated trial (ITT and optionally a subgroup) | sim_region_metrics |
| Simulate Survival Data from AFT Data Generating Mechanism | simulate_from_dgm |
| Simulate Trial Data from GBSG DGM | simulate_from_gbsg_dgm |
| Simulate Trial Data from a GLM Data Generating Mechanism | simulate_from_glm_dgm |
| Sort Subgroups by Focus (post-consistency) | sort_subgroups |
| Cox per-subgroup fit function | subgroup_cox |
| GLM per-subgroup fit function | subgroup_glm |
| Evaluate Subgroup Consistency | subgroup.consistency |
| Subgroup Search for Treatment Effect Heterogeneity (Improved, Parallelized) | subgroup.search |
| Suggest Screening and Consistency Thresholds | suggest_thresholds |
| Summarize Bootstrap Event Counts | summarize_bootstrap_events |
| Enhanced Bootstrap Results Summary | summarize_bootstrap_results |
| Summarize Bootstrap Subgroup Analysis Results | summarize_bootstrap_subgroups |
| Summarise ForestSearch Cross-Validation Diagnostics | summarize_cv_results |
| Summarize Simulation Results | summarize_simulation_results |
| Summary method for cox_ahr_cde objects | summary.cox_ahr_cde |
| Summary method for a DINA fit. | summary.dina |
| Summary Method for forestsearch Objects | summary.forestsearch |
| Summary method for 'fpr_calibration' objects | summary.fpr_calibration |
| Summarize an extreme-subgroups simulation study | summary.subgroup_sims |
| Summary Tables for MRCT Simulation Results | summaryout_mrct |
| Test for Constant Conditional Average Treatment Effect | test_constant_cate |
| Run Both Crump et al. Tests | test_hte |
| HTE Test Using ForestSearch-Selected Covariates | test_hte_from_forestsearch |
| Test for Zero Conditional Average Treatment Effect | test_zero_cate |
| Validate input data for GRF analysis | validate_grf_data |
| Validate k_inter Effect on HR Heterogeneity | validate_k_inter_effect |
| Validate Dataset for MRCT Simulations | validate_mrct_data |
| Validate subgroup definitions against a data frame | validate_subgroups |
| Wilson Score Confidence Interval | wilson_ci |