{
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  "Package": "forestsearch",
  "Title": "Exploratory Subgroup Identification in Clinical Trials with\nSurvival Endpoints",
  "Version": "0.1.0",
  "Authors@R": "person(\"Larry\", \"Leon\", , \"larry.leon.05@post.harvard.edu\", role = c(\"aut\", \"cre\"))",
  "Description": "Implements statistical methods for exploratory subgroup\nidentification in clinical trials with survival endpoints.\nProvides tools for identifying patient subgroups with\ndifferential treatment effects using machine learning\napproaches including Generalized Random Forests (GRF), LASSO\nregularization, and exhaustive combinatorial search algorithms.\nFeatures bootstrap bias correction using infinitesimal\njackknife methods to address selection bias in post-hoc\nanalyses. Designed for clinical researchers conducting\nexploratory subgroup analyses in randomized controlled trials,\nparticularly for multi-regional clinical trials (MRCT)\nrequiring regional consistency evaluation. Supports both\naccelerated failure time (AFT) and Cox proportional hazards\nmodels with comprehensive diagnostic and visualization tools.\nMethods are described in León et al. (2024)\n<doi:10.1002/sim.10163>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
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  "URL": "https://github.com/larry-leon/forestsearch,\nhttps://larry-leon.github.io/forestsearch/",
  "BugReports": "https://github.com/larry-leon/forestsearch/issues",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libxml2-dev\nlibssl-dev libnode-dev",
  "Repository": "https://larry-leon.r-universe.dev",
  "Date/Publication": "2026-03-23 22:20:57 UTC",
  "RemoteUrl": "https://github.com/larry-leon/forestsearch",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-23 07:11:10 UTC",
    "User": "root"
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  "Author": "Larry Leon [aut, cre]",
  "Maintainer": "Larry Leon <larry.leon.05@post.harvard.edu>",
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  "_published": "2026-05-23T07:16:21.001Z",
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  "_topics": [
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    "subgroups"
  ],
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    "build_classification_table",
    "build_estimation_table",
    "calibrate_cens_adjust",
    "calibrate_k_inter",
    "check_censoring_dgm",
    "compute_detection_probability",
    "compute_dgm_cde",
    "cox_ahr_cde_analysis",
    "cox_cs_fit",
    "cox_summary",
    "create_dgm_for_mrct",
    "create_forest_theme",
    "create_summary_table",
    "cv_metrics_tables",
    "cv_summary_tables",
    "figure_note",
    "forestsearch",
    "forestsearch_bootstrap_dofuture",
    "forestsearch_Kfold",
    "forestsearch_KfoldOut",
    "forestsearch_tenfold",
    "format_oc_results",
    "generate_aft_dgm_flex",
    "generate_detection_curve",
    "gg_forest",
    "grf.subg.harm.survival",
    "interpret_estimation_table",
    "mrct_region_sims",
    "plot_detection_curve",
    "plot_km_band_forestsearch",
    "plot_sg_weighted_km",
    "plot_spline_treatment_effect",
    "plot_subgroup_results_forestplot",
    "render_forestplot",
    "render_reference_table",
    "run_simulation_analysis",
    "select_best_subgroup",
    "setup_gbsg_dgm",
    "sg_tables",
    "simulate_from_dgm",
    "subgroup.consistency",
    "summarize_bootstrap_events",
    "summarize_bootstrap_results",
    "summarize_simulation_results",
    "validate_k_inter_effect"
  ],
  "_help": [
    {
      "page": "build_classification_table",
      "title": "Build Classification Rate Table from Simulation Results",
      "topics": [
        "build_classification_table"
      ]
    },
    {
      "page": "build_estimation_table",
      "title": "Build Estimation Properties Table from Simulation Results",
      "topics": [
        "build_estimation_table"
      ]
    },
    {
      "page": "calibrate_cens_adjust",
      "title": "Calibrate Censoring Adjustment to Match DGM Reference Distribution",
      "topics": [
        "calibrate_cens_adjust"
      ]
    },
    {
      "page": "calibrate_k_inter",
      "title": "Calibrate k_inter for Target Subgroup Hazard Ratio",
      "topics": [
        "calibrate_k_inter"
      ]
    },
    {
      "page": "check_censoring_dgm",
      "title": "Diagnose Censoring Consistency Between DGM Source Data and Simulated Data",
      "topics": [
        "check_censoring_dgm"
      ]
    },
    {
      "page": "compute_detection_probability",
      "title": "Compute Probability of Detecting True Subgroup",
      "topics": [
        "compute_detection_probability"
      ]
    },
    {
      "page": "compute_dgm_cde",
      "title": "Compute and Attach CDE Values to a DGM Object",
      "topics": [
        "compute_dgm_cde"
      ]
    },
    {
      "page": "cox_ahr_cde_analysis",
      "title": "Comprehensive Wrapper for Cox Spline Analysis with AHR and CDE Plotting",
      "topics": [
        "cox_ahr_cde_analysis"
      ]
    },
    {
      "page": "cox_cs_fit",
      "title": "Fit Cox Model with Cubic Spline for Treatment Effect Heterogeneity",
      "topics": [
        "cox_cs_fit"
      ]
    },
    {
      "page": "cox_summary",
      "title": "Cox model summary for subgroup (OPTIMIZED)",
      "topics": [
        "cox_summary"
      ]
    },
    {
      "page": "create_dgm_for_mrct",
      "title": "Create Data Generating Mechanism for MRCT Simulations",
      "topics": [
        "create_dgm_for_mrct"
      ]
    },
    {
      "page": "create_forest_theme",
      "title": "Create Forest Plot Theme with Size Controls",
      "topics": [
        "create_forest_theme"
      ]
    },
    {
      "page": "create_summary_table",
      "title": "Create Enhanced Summary Table for Baseline Characteristics",
      "topics": [
        "create_summary_table"
      ]
    },
    {
      "page": "cv_metrics_tables",
      "title": "Create Metrics Tables for Cross-Validation Results",
      "topics": [
        "cv_metrics_tables"
      ]
    },
    {
      "page": "cv_summary_tables",
      "title": "Create Summary Tables from forestsearch_KfoldOut Results",
      "topics": [
        "cv_summary_tables"
      ]
    },
    {
      "page": "figure_note",
      "title": "Generate Figure Note for Quarto/RMarkdown",
      "topics": [
        "figure_note"
      ]
    },
    {
      "page": "forestsearch",
      "title": "ForestSearch: Exploratory Subgroup Identification",
      "topics": [
        "forestsearch"
      ]
    },
    {
      "page": "forestsearch_bootstrap_dofuture",
      "title": "ForestSearch Bootstrap with doFuture Parallelization",
      "topics": [
        "forestsearch_bootstrap_dofuture"
      ]
    },
    {
      "page": "forestsearch_Kfold",
      "title": "ForestSearch K-Fold Cross-Validation",
      "topics": [
        "forestsearch_Kfold"
      ]
    },
    {
      "page": "forestsearch_KfoldOut",
      "title": "ForestSearch K-Fold Cross-Validation Output Summary",
      "topics": [
        "forestsearch_KfoldOut"
      ]
    },
    {
      "page": "forestsearch_tenfold",
      "title": "ForestSearch Repeated K-Fold Cross-Validation",
      "topics": [
        "forestsearch_tenfold"
      ]
    },
    {
      "page": "format_oc_results",
      "title": "Format Operating Characteristics Results as GT Table",
      "topics": [
        "format_oc_results"
      ]
    },
    {
      "page": "generate_aft_dgm_flex",
      "title": "Generate Synthetic Survival Data using AFT Model with Flexible Subgroups",
      "topics": [
        "generate_aft_dgm_flex"
      ]
    },
    {
      "page": "generate_detection_curve",
      "title": "Generate Detection Probability Curve",
      "topics": [
        "generate_detection_curve"
      ]
    },
    {
      "page": "gg_forest",
      "title": "ggplot2 / patchwork forest plot",
      "topics": [
        "gg_forest"
      ]
    },
    {
      "page": "grf.subg.harm.survival",
      "title": "GRF Subgroup Identification for Survival Data",
      "topics": [
        "grf.subg.harm.survival"
      ]
    },
    {
      "page": "interpret_estimation_table",
      "title": "Generate Narrative Interpretation of Estimation Properties",
      "topics": [
        "interpret_estimation_table"
      ]
    },
    {
      "page": "mrct_region_sims",
      "title": "MRCT Regional Subgroup Simulation",
      "topics": [
        "mrct_region_sims"
      ]
    },
    {
      "page": "plot_detection_curve",
      "title": "Plot Detection Probability Curve",
      "topics": [
        "plot_detection_curve"
      ]
    },
    {
      "page": "plot_km_band_forestsearch",
      "title": "Plot Kaplan-Meier Survival Difference Bands for ForestSearch Subgroups",
      "topics": [
        "plot_km_band_forestsearch"
      ]
    },
    {
      "page": "plot_sg_weighted_km",
      "title": "Plot Weighted Kaplan-Meier Curves for ForestSearch Subgroups",
      "topics": [
        "plot_sg_weighted_km"
      ]
    },
    {
      "page": "plot_spline_treatment_effect",
      "title": "Plot Spline Treatment Effect Function",
      "topics": [
        "plot_spline_treatment_effect"
      ]
    },
    {
      "page": "plot_subgroup_results_forestplot",
      "title": "Plot Subgroup Results Forest Plot",
      "topics": [
        "plot_subgroup_results_forestplot"
      ]
    },
    {
      "page": "plot.forestsearch",
      "title": "Plot ForestSearch Results",
      "topics": [
        "plot.forestsearch"
      ]
    },
    {
      "page": "print.cox_ahr_cde",
      "title": "Print method for cox_ahr_cde objects",
      "topics": [
        "print.cox_ahr_cde"
      ]
    },
    {
      "page": "print.forestsearch",
      "title": "Print Method for forestsearch Objects",
      "topics": [
        "print.forestsearch"
      ]
    },
    {
      "page": "print.fs_kfold",
      "title": "Print Method for K-Fold CV Results",
      "topics": [
        "print.fs_kfold"
      ]
    },
    {
      "page": "print.fs_tenfold",
      "title": "Print Method for Repeated K-Fold CV Results",
      "topics": [
        "print.fs_tenfold"
      ]
    },
    {
      "page": "print.gbsg_dgm",
      "title": "Print Method for gbsg_dgm Objects",
      "topics": [
        "print.gbsg_dgm"
      ]
    },
    {
      "page": "render_forestplot",
      "title": "Render ForestSearch Forest Plot",
      "topics": [
        "render_forestplot"
      ]
    },
    {
      "page": "render_reference_table",
      "title": "Render Reference Simulation Table as gt",
      "topics": [
        "render_reference_table"
      ]
    },
    {
      "page": "run_simulation_analysis",
      "title": "Run One Simulation Replicate",
      "topics": [
        "run_simulation_analysis"
      ]
    },
    {
      "page": "select_best_subgroup",
      "title": "Select best subgroup based on criterion",
      "topics": [
        "select_best_subgroup"
      ]
    },
    {
      "page": "setup_gbsg_dgm",
      "title": "Set Up a GBSG-Based AFT Data Generating Mechanism",
      "topics": [
        "setup_gbsg_dgm"
      ]
    },
    {
      "page": "sg_tables",
      "title": "Enhanced Subgroup Summary Tables (gt output)",
      "topics": [
        "sg_tables"
      ]
    },
    {
      "page": "simulate_from_dgm",
      "title": "Simulate Survival Data from AFT Data Generating Mechanism",
      "topics": [
        "simulate_from_dgm"
      ]
    },
    {
      "page": "subgroup.consistency",
      "title": "Evaluate Subgroup Consistency",
      "topics": [
        "subgroup.consistency"
      ]
    },
    {
      "page": "summarize_bootstrap_events",
      "title": "Summarize Bootstrap Event Counts",
      "topics": [
        "summarize_bootstrap_events"
      ]
    },
    {
      "page": "summarize_bootstrap_results",
      "title": "Enhanced Bootstrap Results Summary",
      "topics": [
        "summarize_bootstrap_results"
      ]
    },
    {
      "page": "summarize_simulation_results",
      "title": "Summarize Simulation Results",
      "topics": [
        "summarize_simulation_results"
      ]
    },
    {
      "page": "summary.cox_ahr_cde",
      "title": "Summary method for cox_ahr_cde objects",
      "topics": [
        "summary.cox_ahr_cde"
      ]
    },
    {
      "page": "summary.forestsearch",
      "title": "Summary Method for forestsearch Objects",
      "topics": [
        "summary.forestsearch"
      ]
    },
    {
      "page": "validate_k_inter_effect",
      "title": "Validate k_inter Effect on HR Heterogeneity",
      "topics": [
        "validate_k_inter_effect"
      ]
    }
  ],
  "_readme": "https://github.com/larry-leon/forestsearch/raw/HEAD/README.md",
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      "title": "Exploratory Subgroup Identification with ForestSearch",
      "author": "Larry F. León",
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        "Key Findings",
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        "Session Information"
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      "created": "2026-02-16 19:16:12",
      "modified": "2026-03-19 03:46:49",
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