Reproducible Research in R: An advanced workshop on creating collaborative and automated analysis pipelines

Description

Reproducibility and open scientific practices are increasingly being requested or required of scientists and researchers, but training on these practices has not kept pace. This workshop intends to help bridge that gap and covers the fundamentals and workflow of data analysis in R.

This repository contains the lesson, lecture, and assignment material for the workshop, including the website source files and other associated workshop administration and development files. For more detail on the workshop, check out the welcome page.

Tip

This workshop repository was generated from the template-workshop rostools template.

Instructional Design

The lectures and lessons in this workshop are designed to be presented primarily with a participatory live-coding approach. This involves an teacher typing and running code in RStudio in front of the class, while the class follows along using their own computers. Exercises are interspersed in the lesson material, allowing participants to collaboratively work on smaller coding problems for a few minutes. All lesson materials are provided ahead of time on the workshop website for participants to refer to during lectures. Throughout the workshop, participants are in small groups and are encouraged to help each other out in completing the exercises.

Lesson content

The teaching material is found mainly in these locations:

• index.Rmd: Contains the overview of the workshop.
• overview/ folder: Contains the files that give an overview to the course, such as the syllabus and schedule.
• pre-workshop/: Contains the files needed before the workshop, like the pre-workshop tasks.
• sessions/: Contains the files used during the workshop (e.g. code-along material).
• appendix/: Contains the files used to support the workshop, such as code of conduct, changelog, contributing guides, and instructions for teachers.
• slides/: Contains the lecture slides that are rendered into HTML slides from Markdown.

The website is generated with Quarto, so it follows the file and folder structure conventions from that package.

Support and infrastructure files

• .copier-answers.yml: Contains the answers you gave when copying the project from the template. You should not modify this file directly.
• .cz.toml: Commitizen configuration file for managing versions and changelogs.
• .pre-commit-config.yaml: Pre-commit configuration file for managing and running checks before each commit.
• .typos.toml: typos spell checker configuration file.
• .zenodo.json: Structured citation metadata for your project when archived on Zenodo. This is used to add the metadata to Zenodo when a GitHub release has been uploaded to Zenodo.
• justfile: just configuration file for scripting project tasks.
• .editorconfig: Editor configuration file for EditorConfig to maintain consistent coding styles across different editors and IDEs.
• CHANGELOG.md: Changelog file for tracking changes in the project.
• CONTRIBUTING.md: Guidelines for contributing to the project.
• .github/: Contains GitHub-specific files, such as issue and pull request templates, workflows, dependabot configuration, pull request templates, and a CODEOWNERS file.

Contributing

If you are interested in contributing to the workshop material, please refer to the contributing guidelines. For guidelines on how to be a helper or teacher, check out the For teachers page.

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

Contributors

These are the people who have contributed by submitting changes through pull requests 🎉

@lwjohnst86, @AndersAskeland, @signekb, @nestanyol, @Mortendall

Licensing

This project is licensed under the CC-BY-4.0 License.

Re-use

The workshop is largely designed to be taught in the order given, as each session builds off of the previous ones. The easiest way to use this material is to use it as-is, making use of the tips and instructions found throughout this page. The only thing you might want to make as your own would be the slides, however, they are also good enough to use on their own too.

To help with general admin tasks of running the workshop, there is the samwise R package.

Changelog

For a list of changes, see our changelog page.

How to cite the material

Please cite the material as:

Johnston, L. and Askeland, A. (2025) “Reproducible Research in R: An advanced workshop on creating collaborative and automated analysis pipelines”. Zenodo, 6 September. doi:10.5281/zenodo.17067885.

Or as BibTeX:

@misc{johnston_2025_17067885,
    author = {Johnston, Luke and Askeland, Anders},
    title = {Reproducible Research in R: An advanced workshop on creating collaborative and automated analysis pipelines },
    month = sep,
    year = 2025,
    publisher = {Zenodo},
    version = {1.2.0},
    doi = {10.5281/zenodo.17067885},
    url = {https://doi.org/10.5281/zenodo.17067885},
}