weightedsurv/_pkgdown.yml at master · larry-leon/weightedsurv · GitHub

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

template:
  bootstrap: 5
  bootswatch: cosmo

navbar:
  structure:
    left:  [intro, reference, articles]
    right: [search, github]
  components:
github:
      icon: fa-github
      href: https://github.com/larry-leon/weightedsurv

articles:
  - title: "Getting Started"
    desc: >
      Comprehensive examples of weighted survival analysis with the
      GBSG and Rotterdam datasets.
    contents:
      - weightedsurv_examples

  - title: "Methodology"
    desc: >
      Technical details on the statistical methods implemented in
      weightedsurv.
    contents:
      - articles/weightedcox_methodology
      - articles/weightedkm_methodology
      - articles/weightedrmst_methodology

  - title: "Simulation Studies"
    desc: >
      Monte Carlo simulation studies comparing weighted Cox and
      weighted log-rank tests under non-proportional hazards scenarios.
    contents:
      - articles/weightedcox_wald-vs-logrank_simulations

  - title: "Supplementary Analysis Examples"
    desc: >
      Extended worked examples illustrating resampling-based inference
      and advanced applications.
    contents:
      - articles/martingale_resampling_applications

reference:
  - title: "Data Preparation"
    desc: "Create counting-process datasets for survival analysis"
    contents:
      - df_counting
      - get_dfcounting
      - extract_group_data
      - get_event_risk_matrices
      - get_censoring_and_events
      - calculate_risk_event_counts
      - count_weighted
      - risk_weighted

  - title: "Weighted Cox Models"
    desc: "Fit weighted Cox proportional hazards models with resampling inference"
    contents:
      - cox_rhogamma
      - cox_rhogamma_resample
      - cox_score_rhogamma
      - find_cox_root
      - ci_cox
      - score_calculation
      - N_rhogamma

  - title: "Weighted Log-Rank Tests"
    desc: "Weighted log-rank statistics and diagnostics"
    contents:
      - wlr_dhat_estimates
      - wlr_cumulative
      - check_results

  - title: "Kaplan-Meier Estimation"
    desc: "Weighted KM curves, survival differences, and confidence bands"
    contents:
      - KM_diff
      - KM_estimates
      - resampling_survival
      - km_quantile
      - km_quantile_table
      - kmq_calculations
      - check_km_curve

  - title: "KM Plotting"
    desc: "Plot weighted Kaplan-Meier curves with risk tables and annotations"
    contents:
      - plot_weighted_km
      - plot_km
      - plotKM.band_subgroups
      - plot_km_curves_counting
      - plot_km_confint_polygon
      - KM_plot_2sample_weighted_counting
      - add_risk_table
      - add_legends
      - add_median_annotation
      - get_riskpoints

  - title: "RMST"
    desc: "Restricted Mean Survival Time calculations with confidence bands"
    contents:
      - cumulative_rmst_bands

  - title: "Weighting Schemes"
    desc: "Weight function computation, validation, and visualization"
    contents:
      - wt.rg.S
      - get_weights
      - get_validated_weights
      - extract_and_calc_weights
      - validate_scheme_params
      - plot_weight_schemes

  - title: "Baseline Tables"
    desc: "Publication-ready baseline characteristics tables"
    contents:
      - create_baseline_table

  - title: "Utilities"
    desc: "Input validation and formatting helpers"
    contents:
      - validate_input
      - format_pval
      - safe_run