Contributing to phangorn

First of all, thanks for considering contributing to phangorn! 👍 It’s people like you that make it rewarding for us - the project maintainers - to work on phangorn. 😊

phangorn is an open source project, maintained by people who care. We are not directly funded to do so.

How you can contribute

There are several ways you can contribute to this project. If you want to know more about why and how to contribute to open source projects like this one, see this Open Source Guide.

Think phangorn is useful? Let others discover it, by telling them in person, via Twitter or a blog post.

Using phangorn for a paper you are writing? Consider citing it.

Ask a question ⁉️

Using phangorn and got stuck? Browse the documentation to see if you can find a solution. Still stuck? Post your question as an issue on GitHub. While we cannot offer user support, we’ll try to do our best to address it, as questions often lead to better documentation or the discovery of bugs.

Want to ask a question in private? Contact the package maintainer by [email][mailto:email].

Propose an idea 💡

Have an idea for a new phangorn feature? Take a look at the documentation and issue list to see if it isn’t included or suggested yet. If not, suggest your idea as an issue on GitHub. While we can’t promise to implement your idea, it helps to:

Explain in detail how it would work.
Keep the scope as narrow as possible.

See below if you want to contribute code for your idea as well.

Report a bug 🐛

Using phangorn and discovered a bug? That’s annoying! Don’t let others have the same experience and report it as an issue on GitHub so we can fix it. A good bug report makes it easier for us to do so, so please include:

Your operating system name and version (e.g. Mac OS 10.13.6).
Any details about your local setup that might be helpful in troubleshooting.
Detailed steps to reproduce the bug.

Improve the documentation 📖

Noticed a typo on the website? Think a function could use a better example? Good documentation makes all the difference, so your help to improve it is very welcome!

The website

This website is generated with pkgdown. That means we don’t have to write any html: content is pulled together from documentation in the code, vignettes, Markdown files, the package DESCRIPTION and _pkgdown.yml settings. If you know your way around pkgdown, you can propose a file change to improve documentation. If not, report an issue and we can point you in the right direction.

Function documentation

Functions are described as comments near their code and translated to documentation using roxygen2. If you want to improve a function description:

Go to R/ directory in the code repository.
Look for the file with the name of the function.
Propose a file change to update the function documentation in the roxygen comments (starting with #').

Contribute code 📝

Care to fix bugs or implement new functionality for phangorn? Awesome! 👏 Have a look at the issue list and leave a comment on the things you want to work on. See also the development guidelines below.

Development guidelines

We try to follow the GitHub flow for development.

Fork this repo and clone it to your computer. To learn more about this process, see this guide.
If you have forked and cloned the project before and it has been a while since you worked on it, pull changes from the original repo to your clone by using git pull upstream main.
Open the RStudio project file (.Rproj).
Make your changes:
- Write your code.
- Test your code (bonus points for adding unit tests).
- Document your code (see function documentation above).
- Check your code with devtools::check() and aim for 0 errors and warnings.
Commit and push your changes.
Submit a pull request.