CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with this repository.

Repository Overview

[Brief description of what this project does, its purpose, and key goals]

Key Dependencies

Package Location/Version Purpose
BATON ~/Downloads/BATON Bayesian optimization for adaptive trials
evolveTrial ~/Downloads/evolveTrial Adaptive trial simulations
tidyverse CRAN ≥2.0 Data manipulation
Quarto System ≥1.4 Document rendering 
# Install local packages
devtools::install("~/Downloads/BATON")
devtools::install("~/Downloads/evolveTrial")

Common Commands

Build/Render

make pdf          # Render to PDF
make html         # Render to HTML
make quick        # Quick build with caching

Testing

make test         # Run all validation tests
Rscript tests/run_tests.R  # R tests only

Simulations

# Run production scenarios
Rscript scripts/run_scenarios.R scenarios/production.csv

# Dry run to validate
Rscript scripts/run_scenarios.R scenarios/production.csv --dry-run

Environment Variables

Variable Default Purpose
BO_BUDGET 120 Total evaluation budget
QUICK_MODE 0 Enable quick mode (1=on)

Architecture

Directory Structure

├── R/              # Shared R functions and utilities
├── scripts/        # Executable scripts
├── manuscript/     # Quarto manuscript source
├── scenarios/      # CSV scenario specifications
├── results/        # Output files (gitignored)
├── figures/        # Generated figures
├── docs/           # Documentation
└── tests/          # Validation tests

Key Files

File Purpose
_targets.R Pipeline definition
globals.yml Central configuration
R/utils.R Shared utility functions
CODING_STANDARDS.md Style guide

Coding Conventions

R Style

  • Tidyverse style guide
  • Two-space indentation
  • snake_case for functions and variables
  • library() calls at top of scripts
  • Explicit return() statements

Parameter Naming

Concept Correct Incorrect
Maximum sample size total_n nmax, N
Type I error type1 alpha
Type II error type2 beta
Power power 1-beta

Commits

  • Conventional commits: feat:, fix:, docs:, refactor:
  • Reference issues: fixes #123
  • Atomic commits (one logical change)

Seeds

Always record seeds for reproducibility:

set.seed(2025)  # Seed for [purpose]

Testing & Validation

  • Use deterministic seeds
  • Validate both fidelity = "low" and "high" paths
  • Check plausible ranges (power 0.70-0.95, type I 0.01-0.15)

Documentation Index

Document Purpose
docs/QUICK_START.md Getting started guide
CODING_STANDARDS.md Full style guide
CHANGELOG.md Version history
AGENTS.md CI/CD and automation