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Contributing to GeoTox

This outlines how to (1) propose a change to GeoTox and (2) serves as log of potential enhancements for GeoTox.

Best Practices

If you’ve found a bug, please file an issue that illustrates the bug with a minimal reprex (this will also help you write a unit test, if needed). See tidyverse team’s guide on how to create a great issue for more advice. When adding a new function to the package, always add working examples of the new function in roxygen2 documentation under #' @examples.

Pull request process

  • Fork the package and clone onto your computer. If you haven’t done this before, we recommend using usethis::create_from_github("NIEHS/GeoTox", fork = TRUE).

  • Install all development dependencies with devtools::install_dev_deps(), and then make sure the package passes R CMD check by running devtools::check(). If R CMD check doesn’t pass cleanly, it’s a good idea to ask for help before continuing.

  • Create a Git branch for your pull request (PR). We recommend using usethis::pr_init("brief-description-of-change").

  • Make your changes, commit to git, and then create a PR by running usethis::pr_push(), and following the prompts in your browser. The title of your PR should briefly describe the change. The body of your PR should contain Fixes #issue-number.

  • For user-facing changes, add a bullet to the top of NEWS.md (i.e. just below the first header).

Code style

  • Please abide by 80-character line rules (as default settings in lintr)

  • We use roxygen2, with Markdown syntax, for documentation.

  • We use testthat for unit tests. Contributions with test cases included are easier to accept.

Fixing typos

You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the source file. This generally means you’ll need to edit roxygen2 comments in an .R, not a .Rd file. You can find the .R file that generates the .Rd by reading the comment in the first line.

GeoTox Open Issues and Enhancements

This section serves as log of potential enhancements for GeoTox. Community members are welcomed and encouraged to use our contributing guide to address the open issues and enhancements to this package. Additionally, new enhancements can be proposed by using our enhancements template request. If you want to address an open enchancement or suggest a new one, it’s a good idea to first file an issue and make sure someone from the team agrees that it’s needed.

Scientific

  1. Non-steady state toxicokinetics. This will likely require additional usage of the httk package.
  2. Complete integration of the multiple end-point analysis into the GeoTox objects
  3. Integration of Reflected Generalized Concentration Addition (RGCA), which will allow 3+ parameter hill models to be used for additive mixture predictions.
  4. Benchmark Dose modeling (BMD) as a metric for risk assessment. Suggested ingetrations include BMDexpress2.0 or transcryptR - note transcryptR is also currently a Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.

Computational

  1. targets pipeline template. If we provide a make-like targets pipeline, then new users will have a reproducible template to run their analysis with ease.

Code of Conduct

Please note that the chopin project is released with a Contributor Code of Conduct. By contributing to this project you agree to abide by its terms.