claude-r-dev

Supercharge your R package development with AI-powered workflows using Claude Code

claude-r-dev is a comprehensive configuration system for Claude Code that transforms AI-assisted coding from helpful suggestions into systematic, production-ready R package development.

✨ What You Get

🔧 Modular Profiles: Mix and match configurations for your package type
🤖 Specialized Sub-Agents: Expert AI assistants for code review, testing, and more
⚡ Custom Workflows: Slash commands for common development tasks
📊 Quality Automation: Built-in checks for CRAN compliance, test coverage, style
🎓 Best Practices: Embedded standards from R package development, statistical methodology, and software engineering
🚀 One-Line Install: From GitHub directly to your package

🚀 Quick Start

Install Claude Code CLI

npm install -g @anthropic-ai/claude-code

Install claude-r-dev to Your Package

Option 1: One-liner (recommended)

curl -fsSL https://raw.githubusercontent.com/Data-Wise/claude-r-dev/main/scripts/install.sh | bash -s -- \
  --profile base \
  --target /path/to/your/package

Option 2: With multiple profiles

# For statistical methodology packages
bash <(curl -fsSL https://raw.githubusercontent.com/Data-Wise/claude-r-dev/main/scripts/install.sh) \
  --profiles base,statistical-methods \
  --target ~/projects/mypackage

Option 3: Clone and customize

git clone https://github.com/Data-Wise/claude-r-dev.git
cd claude-r-dev
./scripts/install.sh --profiles base,statistical-methods --target ~/mypackage

Start Using

cd /path/to/your/package
claude

# Try these commands:
/permissions              # View configured tools
/project:                 # See available slash commands
/project:pre-commit-check # Run comprehensive quality checks

🎨 Create Your Custom Configuration

NEW: Interactive wizard to generate package-specific configurations!

cd your-package
claude

/project:init

The wizard asks about:

Package type and domain
Statistical notation preferences
Object system (S3, S4, S7, R6)
Function organization
Inference methods
Testing requirements
Website design (5 color schemes!)

...and generates a custom configuration tailored to YOUR package!

Learn more about customization →

📦 Available Profiles

🔧 base (Required)

Essential R package development standards

CRAN compliance automation
Testing standards (testthat3, >80% coverage)
Code style enforcement (tidyverse)
Git workflows and best practices
Documentation standards (roxygen2, pkgdown)

Includes:

/project:fix-bug - Structured debugging workflow
/project:pre-commit-check - Comprehensive quality checks
r-package-reviewer sub-agent - Expert code review
test-specialist sub-agent - Comprehensive test generation

📊 statistical-methods

For methodology and causal inference packages

Statistical notation standards (VanderWeele, Pearl, Hernán & Robins)
Identification assumptions documentation
Sensitivity analysis patterns
Simulation study workflows
S7 object system guidelines

Includes:

/project:add-method - Systematic new method development
/project:migrate-s7 - Safe S3/S4 to S7 migration
Enhanced r-package-reviewer with statistical correctness checks
Methods-specific testing patterns

📈 data-analysis (Coming in v1.4)

For packages focused on data analysis and visualization

🌐 shiny (Coming in v1.4)

For Shiny application packages

🧬 bioconductor (Coming in v1.4)

For Bioconductor package development

See all profiles →

💡 Usage Examples

Basic Package Development

# Install base profile
./scripts/install.sh --profile base --target ~/mypackage
cd ~/mypackage
claude

# In Claude Code:
"Read the package structure and suggest improvements"
/project:pre-commit-check
/project:fix-bug "function X fails with negative inputs"

Statistical Methods Package

# Install base + statistical-methods
./scripts/install.sh --profiles base,statistical-methods --target ~/causalmethod
cd ~/causalmethod
claude

# In Claude Code:
/project:add-method "doubly-robust-mediation"
# Follows guided workflow: Plan → Test → Implement → Document

"Use r-package-reviewer sub-agent to check statistical correctness"
# Reviews formulas, assumptions, inference methods

/project:migrate-s7 MediationResult
# Safely migrates S3/S4 classes to modern S7

Test-Driven Development

"Use test-specialist to write comprehensive tests for my_function()"
# Generates tests for happy path, edge cases, validation

/project:pre-commit-check
# Ensures >80% coverage, style compliance, R CMD check passes

"Commit these changes with a descriptive message"
# Claude writes commit following conventional commits standard

🎯 Key Features

Custom Slash Commands

Execute complex workflows with simple commands:

/project:add-method - Add new statistical/analytical methods
/project:fix-bug - Test-first debugging workflow
/project:migrate-s7 - S3/S4 to S7 class migration
/project:pre-commit-check - Full quality assurance suite

Specialized Sub-Agents

Expert AI assistants that maintain focused context:

r-package-reviewer: Reviews for statistical correctness, CRAN compliance, code quality
test-specialist: Writes comprehensive test suites with edge cases
documentation-writer: Creates roxygen2 docs, vignettes, pkgdown sites

Automated Quality Checks

Built-in automation for:

✅ Style checking (styler, lintr)
✅ Test coverage (covr, >80% required)
✅ R CMD check (CRAN compliance)
✅ Documentation completeness
✅ Spelling and grammar
✅ Git commit message standards

Statistical Rigor

For methodology packages:

Standard notation (VanderWeele 2015, Pearl 2009)
Identification assumptions documentation
Inference method requirements (bootstrap, delta method)
Sensitivity analysis integration
Edge case testing (missing data, collinearity, etc.)

📚 Documentation

Documentation Site: https://data-wise.github.io/claude-r-dev/

Getting Started - Installation and first steps
Profiles Guide - Available profiles and features
Customization - Wizard and manual customization
Commands Reference - All commands and agents
Config Schema - Configuration file reference
Contributing - How to contribute
Tutorials - Step-by-step guides
Examples - Example configurations
Changelog - Version history

🏗️ Architecture

Profile System

base/                   # Core R package standards (required)
├── CLAUDE.md          # Main configuration
├── settings.json      # Tool permissions
├── commands/          # Slash commands
└── agents/            # Sub-agents

statistical-methods/    # Extends base for methodology
├── CLAUDE.md          # Additional standards
├── commands/          # Methods-specific commands
└── agents/            # Enhanced reviewers

Installation Process

Validates target is R package (checks for DESCRIPTION)
Backs up existing configuration
Installs base profile
Merges additional profiles
Updates .gitignore
Generates installation report

🔧 Requirements

Essential

Claude Code CLI: npm install -g @anthropic-ai/claude-code
R (≥ 4.0.0): With development tools
Git: For version control

R Packages (installed automatically on first use)

install.packages(c(
  "devtools", "testthat", "roxygen2",
  "styler", "lintr", "covr", "pkgdown",
  "goodpractice", "spelling", "usethis"
))

For statistical-methods profile:

install.packages("S7")  # Modern object system

🤝 Contributing

We welcome contributions! Ways to help:

Add new profiles: Create configurations for new package types
Improve existing profiles: Enhance standards and workflows
Submit slash commands: Share useful workflow automations
Create sub-agents: Build specialized AI assistants
Improve documentation: Clarify usage and examples
Report issues: Help us identify problems
Share feedback: Tell us what works and what doesn't

See CONTRIBUTING.md for details.

📊 Real-World Examples

mediationverse

Statistical methods package for causal mediation analysis using claude-r-dev:

Profiles: base + statistical-methods
Result: 50% faster feature development, 100% test coverage

[Your Package Here]

Successfully using claude-r-dev? Submit a PR to share your story!

🎓 Learning Resources

🗺️ Roadmap

v1.0 (Current)

✅ Base profile with core R package development
✅ Statistical-methods profile for methodology packages
✅ Smart installer with profile merging
✅ Comprehensive documentation

v1.1 (Next)

⬜ Data-analysis profile
⬜ Shiny profile
⬜ Bioconductor profile
⬜ Profile update system
⬜ Community profile registry

v1.2 (Future)

⬜ Web-based profile builder
⬜ VS Code extension integration
⬜ GitHub Actions workflow templates
⬜ Team collaboration features

❓ FAQ

Q: Do I need Claude Pro to use this?
A: No, Claude Code works with any Claude account. Pro provides extended thinking, but is not required.

Q: Can I use this with Cursor or other AI coding tools?
A: The configuration is optimized for Claude Code, but many patterns can be adapted.

Q: Will this work with my existing package?
A: Yes! The installer checks for existing configurations and merges intelligently.

Q: Can I customize the profiles?
A: Absolutely! See Customization Guide for details.

Q: How do I update to the latest version?
A: Run ./scripts/update.sh in your package, or reinstall with the latest version.

Q: Is this only for R packages?
A: Currently yes, but the architecture could support other languages. Contributions welcome!

📝 License

MIT License - see LICENSE for details.

🙏 Acknowledgments

Anthropic - For Claude Code and best practices documentation
R Core Team - For R and package development infrastructure
Hadley Wickham - For R package development standards and tidyverse
Contributors - Everyone who improves and extends claude-r-dev

📬 Contact & Support

Issues: GitHub Issues
Discussions: GitHub Discussions

Transform your R package development from ad-hoc to systematic, from uncertain to rigorous, from solo to AI-collaborative.

Install. Configure. Excel. 🚀

Made with ❤️ for the R community

Name		Name	Last commit message	Last commit date
Latest commit History 17 Commits
.github/workflows		.github/workflows
docs		docs
docs_mkdocs		docs_mkdocs
examples		examples
profiles		profiles
scripts		scripts
CHANGELOG.md		CHANGELOG.md
CONTRIBUTING.md		CONTRIBUTING.md
IMPLEMENTATION_PLAN.md		IMPLEMENTATION_PLAN.md
LICENSE		LICENSE
MKDOCS_TUTORIAL.md		MKDOCS_TUTORIAL.md
PROJECT_SUMMARY.md		PROJECT_SUMMARY.md
README.md		README.md
ROADMAP.md		ROADMAP.md
TESTING_PLAN.md		TESTING_PLAN.md
UPDATE_SUMMARY.md		UPDATE_SUMMARY.md
mkdocs.yml		mkdocs.yml

License

Data-Wise/claude-r-dev

Folders and files

Latest commit

History

Repository files navigation