Contributing to sAMRat

Thank you for your interest in contributing to sAMRat — a Shiny app for antimicrobial resistance analysis. This file gives a brief, practical guide to reporting issues, submitting changes, and running basic checks locally.

Quick start

• Fork the repository and create a branch named X-feature/your-short-desc or X-fix/your-short-desc. Replace X with the respective issue number.
• Make small, focused commits with clear messages.
• Open a pull request (PR) against the main branch. Describe the problem, your approach, and any testing you ran.

Reporting issues

• Use the GitHub Issues page to report bugs or request features. Provide a minimal reproducible example and any error messages or screenshots.

Development tips

• This is an R package and a Shiny app. Follow standard R package practices where possible.
• Keep changes small and well-scoped.

Coding style

• Prefer the tidyverse style for R code (e.g., consistent indentation, use of pipes). Keep functions small and documented with roxygen2 comments.

Tests

• Tests live under tests/testthat/. Add tests for new behavior and ensure existing tests still pass.
• Run tests locally in your R console with:

devtools::test()

Checks and documentation

• Run a package check before opening a PR:

devtools::check()

• If you modify exported functions or add new ones, update roxygen documentation and rebuild the NAMESPACE:

roxygen2::roxygenise()

Pull request checklist

• PR targets main branch (or follow repo-specific branch policy)
• Adds or updates tests where applicable
• Passes devtools::check() with no new NOTE/ERRORs if possible
• Includes an entry in NEWS.md or the changelog if appropriate

Code of conduct

Please follow the project’s code of conduct (be respectful and constructive). If the project does not yet include a CODE_OF_CONDUCT.md, follow GitHub’s default community guidelines.

Questions or contact

For questions or help getting started, open an issue or email the package maintainer listed in DESCRIPTION.

Thanks for helping improve sAMRat — contributions are welcome and appreciated!