_pkgdown.yml

# =============================================================================
# _pkgdown.yml - forestsearch Package Documentation Website Configuration
# =============================================================================
#
# Build the site with: pkgdown::build_site()
# Preview locally with: pkgdown::preview_site()
# Validate with:  pkgdown::check_pkgdown()
#
# =============================================================================

url: https://larry-leon.github.io/forestsearch

template:
  bootstrap: 5
  bootswatch: flatly
  bslib:
    primary: "#0d6efd"
    border-radius: 0.5rem
    btn-border-radius: 0.25rem

home:
  title: forestsearch
  description: >
    Exploratory subgroup identification in clinical trials with survival
    endpoints using bootstrap bias correction.

navbar:
  structure:
    left:  [intro, reference, articles, news]
    right: [search, github]
  components:
    intro:
      text: Getting Started
      href: articles/forestsearch.html
    reference:
      text: Reference
      href: reference/index.html
    articles:
      text: Articles
      menu:
        - text: Introduction to forestsearch
          href: articles/forestsearch.html
        - text: "---"
        - text: Methodology
          href: articles/methodology.html
        - text: Treatment Effect Definitions
          href: articles/treatment_effect_definitions.html
        - text: Biomarker Treatment Effects
          href: articles/biomarker_effects.html
        - text: Causal Interpretation of Hazard Ratios
          href: articles/causal_effects_brief_review.html
        - text: Simulation Studies
          href: articles/paper_simulations.html
        - text: Extreme Subgroup Effects
          href: articles/extreme_subgroups.html
    news:
      text: Changelog
      href: news/index.html
    github:
      icon: fa-github
      href: https://github.com/larry-leon/forestsearch
      aria-label: GitHub

# =============================================================================
# REFERENCE - organized by functional area (53 exported functions)
# =============================================================================

reference:
  # ---------------------------------------------------------------------------
  # CORE ALGORITHM
  # ---------------------------------------------------------------------------
  - title: "Core Algorithm"
    desc: >
      Main forestsearch function, subgroup selection, and consistency
      evaluation.
    contents:
      - forestsearch
      - print.forestsearch
      - summary.forestsearch
      - plot.forestsearch
      - select_best_subgroup
      - subgroup.consistency

  # ---------------------------------------------------------------------------
  # BOOTSTRAP INFERENCE
  # ---------------------------------------------------------------------------
  - title: "Bootstrap Bias Correction"
    desc: >
      Bootstrap methods for bias-corrected hazard ratio estimation using
      infinitesimal jackknife variance estimation (Leon et al., 2024).
    contents:
      - forestsearch_bootstrap_dofuture
      - summarize_bootstrap_results
      - summarize_bootstrap_events

  # ---------------------------------------------------------------------------
  # CROSS-VALIDATION
  # ---------------------------------------------------------------------------
  - title: "Cross-Validation"
    desc: >
      K-fold and repeated cross-validation for assessing subgroup
      identification stability and agreement metrics.
    contents:
      - forestsearch_Kfold
      - forestsearch_tenfold
      - forestsearch_KfoldOut
      - cv_summary_tables
      - cv_metrics_tables
      - print.fs_kfold
      - print.fs_tenfold

  # ---------------------------------------------------------------------------
  # GRF INTEGRATION
  # ---------------------------------------------------------------------------
  - title: "GRF Integration"
    desc: >
      Generalized Random Forest methods for heterogeneous treatment
      effect estimation and variable importance screening.
    contents:
      - grf.subg.harm.survival

  # ---------------------------------------------------------------------------
  # COX MODEL UTILITIES
  # ---------------------------------------------------------------------------
  - title: "Cox Model Utilities"
    desc: >
      Cox proportional hazards model wrappers with robust standard errors,
      spline fitting, and average hazard ratio calculations.
    contents:
      - cox_summary
      - cox_ahr_cde_analysis
      - print.cox_ahr_cde
      - summary.cox_ahr_cde
      - cox_cs_fit

  # ---------------------------------------------------------------------------
  # SUBGROUP TABLES & ESTIMATES
  # ---------------------------------------------------------------------------
  - title: "Subgroup Tables & Estimates"
    desc: >
      Formatted tables of subgroup estimates.
    contents:
      - sg_tables
      - create_summary_table

  # ---------------------------------------------------------------------------
  # VISUALIZATION
  # ---------------------------------------------------------------------------
  - title: "Visualization"
    desc: >
      Publication-ready plotting functions for forest plots, survival curves,
      subgroup characteristics, and detection probability curves.
    contents:
      - gg_forest
      - plot_subgroup_results_forestplot
      - render_forestplot
      - create_forest_theme
      - plot_km_band_forestsearch
      - plot_sg_weighted_km
      - figure_note
      - plot_spline_treatment_effect
      - plot_detection_curve

  # ---------------------------------------------------------------------------
  # DATA GENERATING MECHANISMS
  # ---------------------------------------------------------------------------
  - title: "Data Generating Mechanisms"
    desc: >
      Functions for creating data generating mechanisms (DGMs) for
      simulation studies with configurable treatment effect heterogeneity.
    contents:
      - generate_aft_dgm_flex
      - setup_gbsg_dgm
      - print.gbsg_dgm
      - compute_dgm_cde
      - simulate_from_dgm
      - calibrate_cens_adjust
      - check_censoring_dgm
      - calibrate_k_inter
      - validate_k_inter_effect

  # ---------------------------------------------------------------------------
  # SIMULATION STUDIES
  # ---------------------------------------------------------------------------
  - title: "Simulation Studies"
    desc: >
      Running and summarizing simulation studies for operating characteristics.
    contents:
      - run_simulation_analysis
      - summarize_simulation_results
      - format_oc_results
      - build_classification_table
      - build_estimation_table
      - interpret_estimation_table
      - render_reference_table
      - compute_detection_probability
      - generate_detection_curve

  # ---------------------------------------------------------------------------
  # MULTI-REGIONAL CLINICAL TRIALS
  # ---------------------------------------------------------------------------
  - title: "Multi-Regional Clinical Trials"
    desc: >
      Specialized functions for multi-regional clinical trial (MRCT)
      subgroup analysis with regional consistency evaluation.
    contents:
      - mrct_region_sims
      - create_dgm_for_mrct

  # ---------------------------------------------------------------------------
  # INTERNAL
  # ---------------------------------------------------------------------------
  - title: "Internal"
    desc: >
      Internal implementation details. These functions are not intended to
      be called directly by users.
    contents:
      - has_keyword("internal")

# =============================================================================
# ARTICLES (VIGNETTES)
# =============================================================================

articles:
  - title: Getting Started
    navbar: ~
    contents:
      - forestsearch

  - title: Methodology
    desc: Technical details on the statistical methods
    contents:
      - "articles/methodology"

  - title: Treatment Effect Definitions
    desc: >
      Definitions and computation of marginal HR, average hazard ratio
      (AHR), and controlled direct effect (CDE) estimands.
    contents:
      - "articles/treatment_effect_definitions"
      - "articles/biomarker_effects"
      - "articles/causal_effects_brief_review"

  - title: Simulation Studies
    desc: Operating characteristics and published benchmarks
    contents:
      - "articles/paper_simulations"
      - "articles/extreme_subgroups"

# =============================================================================
# NEWS
# =============================================================================

news:
  one_page: true
  cran_dates: false

# =============================================================================
# ADDITIONAL OPTIONS
# =============================================================================

development:
  mode: auto

figures:
  dev: ragg::agg_png
  dpi: 96
  dev.args: []
  fig.ext: png
  fig.width: 7.2916667
  fig.height: ~
  fig.retina: 2
  fig.asp: 1.618
  bg: NA
  other.parameters: []

code:
  width: 80

footer:
  structure:
    left: developed_by
    right: built_with