Contributing to EpiAwareR

Thank you for your interest in contributing to EpiAwareR! This document provides guidelines for contributing to the project.

Code of Conduct

By participating in this project, you agree to maintain a respectful and inclusive environment for all contributors.

Types of Contributions

Bug Reports

If you find a bug, please open an issue with:

• A clear, descriptive title
• A minimal reproducible example
• Your R and Julia versions (sessionInfo() output)
• Expected vs. actual behavior

Feature Requests

We welcome suggestions for new features! Please:

• Check if the feature already exists in the Julia EpiAware package
• Describe the use case and expected behavior
• Consider whether it should be a dedicated R wrapper or accessible via epiaware_call()

Code Contributions

1. Fork and clone the repository
2. Create a branch for your changes: git checkout -b feature/my-feature
3. Make your changes following the code style below
4. Add tests for any new functionality
5. Update documentation including roxygen2 comments
6. Run checks: devtools::check()
7. Submit a pull request with a clear description

Development Setup

Prerequisites

• R >= 4.0.0
• Julia >= 1.9.0
• Development tools:
  • devtools: install.packages("devtools")
  • roxygen2: install.packages("roxygen2")
  • testthat: install.packages("testthat")

Setup

# Clone the repository
git clone https://github.com/CDCgov/Rt-without-renewal.git
cd Rt-without-renewal/EpiAwareR

# Load package for development
devtools::load_all()

# Set up Julia
epiaware_setup_julia()

Code Style

R Code Style

Follow standard R conventions:

• Function names: snake_case for user-facing functions
• Internal functions: Prefix with . (e.g., .internal_helper)
• Variable names: snake_case
• Constants: SCREAMING_SNAKE_CASE
• Line length: Maximum 80 characters when practical
• Indentation: 2 spaces (no tabs)

Documentation

All exported functions must have roxygen2 documentation:

#' Brief Title
#'
#' Detailed description of what the function does.
#'
#' @param param1 Description of param1
#' @param param2 Description of param2
#'
#' @return Description of return value
#'
#' @examples
#' \dontrun{
#' # Example usage
#' result <- my_function(param1 = 1, param2 = 2)
#' }
#'
#' @export
my_function <- function(param1, param2) {
  # Implementation
}

S3 Classes

EpiAwareR uses S3 classes for simplicity:

• Constructor pattern: Validate inputs, call Julia, return structured list with julia_ref
• Class inheritance: Use multiple inheritance (e.g., c("epiaware_ar", "epiaware_latent", "epiaware_model"))
• Print methods: Always provide informative print() methods

Testing

Writing Tests

• Place tests in tests/testthat/test-*.R
• Use descriptive test names: test_that("function validates inputs", { ... })
• Test edge cases and error conditions
• Skip long-running tests with skip_on_cran()
• Skip tests requiring Julia with skip_if_not(epiaware_available())

Running Tests

# Run all tests
devtools::test()

# Run specific test file
testthat::test_file("tests/testthat/test-components.R")

# Check package
devtools::check()

Adding New Components

Adding a New Wrapped Component

1. Create constructor function in appropriate file (e.g., R/latent-models.R)
2. Validate inputs in R
3. Convert distributions using .to_julia_dist()
4. Call Julia constructor using .call_julia_function()
5. Return S3 object with proper class inheritance
6. Add print method
7. Write tests in tests/testthat/
8. Update documentation in README and vignettes
9. Add examples to function documentation

Example structure:

#' My New Model
#'
#' @param param1 Description
#' @export
MyNewModel <- function(param1) {
  # Validate
  if (!is.numeric(param1)) stop("param1 must be numeric")

  # Convert to Julia
  julia_obj <- .call_julia_function("MyNewModel", param1 = param1)

  # Return S3 object
  structure(
    list(julia_ref = julia_obj, spec = list(param1 = param1)),
    class = c("epiaware_mynew", "epiaware_latent", "epiaware_model")
  )
}

#' @export
print.epiaware_mynew <- function(x, ...) {
  cat("<EpiAware My New Model>\n")
  cat("  Param1:", x$spec$param1, "\n")
  invisible(x)
}

Adding Access to Julia Features

For features not yet wrapped, users can use epiaware_call():

custom_model <- epiaware_call("JuliaFunction", param1 = value1)

Document these in the function reference with guidance on when explicit wrappers are warranted.

Documentation

Regenerating Documentation

# Update roxygen documentation
devtools::document()

# Build vignettes
devtools::build_vignettes()

Building README

If README.Rmd exists:

# Knit README
knitr::knit("README.Rmd")

Release Process

1. Update version in DESCRIPTION
2. Update NEWS.md with changes
3. Run devtools::check() with no errors, warnings, or notes
4. Build and check package: devtools::check()
5. Submit to CRAN or create GitHub release

Questions?

If you have questions about contributing:

• Open a discussion on GitHub
• Contact the package maintainer: sebastian.funk@lshtm.ac.uk
• Refer to the EpiAware Julia documentation

License

By contributing, you agree that your contributions will be licensed under the MIT License.