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Package Architecture

Source: vignettes/architecture.Rmd
architecture.Rmd

Overview

The goldilocks package implements the Goldilocks adaptive trial design described in Broglio et al. (2014). This vignette provides a visual overview of how the package functions are interconnected.

Function dependency diagram

The diagram below shows the call graph from the top-level simulation function (sim_trials()) down through the core engine (survival_adapt()) and into the internal analysis pipeline.

Exported functions are shown in blue. Internal functions are shown in grey.

Function roles

The functions fall into three layers:

Simulation layer

  • sim_trials(): Top-level entry point. Runs survival_adapt() across multiple trials (optionally in parallel) and collates results.
  • summarise_sims(): Summarizes the output of sim_trials(), computing operating characteristics such as power, expected sample size, and stopping probabilities.

Trial engine

  • survival_adapt(): Simulates a single adaptive trial. Generates data via sim_comp_data(), conducts interim analyses using posterior() and test_stop_success(), and performs the final analysis via test_final().

Data generation and analysis utilities

  • sim_comp_data(): Generates a complete trial dataset by calling enrollment(), randomization(), and pwe_sim().
  • posterior(): Estimates the posterior distribution of piecewise exponential hazard rates using a conjugate Gamma model.
  • analyse_data(): Applies the chosen analysis method (logrank, cox, bayes, or chisq) to an (imputed) dataset.
  • impute_data(): Imputes missing event times for censored subjects using pwe_impute() or pwe_sim().
  • haz_to_prop(): Converts posterior hazard rate draws to cumulative incidence proportions via ppwe().