6. Conclusion and next steps
6.1 Concluding Remarks
Great job in making it to the end of this module! Along the way we hope you haved:
- Developed an appreciation for the need and principles of Literate Programming (LP) in research
- Acquired some new skills in Markdown and conducting LP using R/RStudio and Quarto
As with most technical skills, mastery requires practice, practice and more practice. We hope the lessons here have prepared you to adopt an LP approach for your next project!
For those who want a deeper dive or learn more about a specifc aspect of this course, below is a selection our favourite links on learning Literate Programming, Markdown, and LP with RStudio/Quarto. Additionally, this course is the first part in a multi-series programme on implementing code reproducibility for research. Links and brief descriptions of further course in the series can be found further below.
6.2 Further Resources on Literate Programming with RStudio/Quarto
Below are some of our favourite links, ranging from from comprehensive references to short tutorials.
| Content | Description | Link |
|---|---|---|
| Markdown Essentials | This Markdown Guide offers a short and handy reference to the basic syntax or grammar of markdown. | https://www.markdownguide.org/basic-syntax/ |
| Markdown Practice | Want to practise some more markdown? Try this excellent, standalone Markdown tutorial. | https://www.markdowntutorial.com/ |
| Markdown Cheatsheet | Because sometimes, a concise cheatsheet is all you need… | https://www.markdownguide.org/cheat-sheet/ |
| RMarkdown Cheatsheet | A handy cheatsheet for the R extension for Markdown (RMarkdown) | https://shiny.posit.co/r/articles/build/rm-cheatsheet/ |
| RMarkdown Cookbook | Complete guide for RMarkdown that can be extended to Quarto documents with slight syntax modifications | https://bookdown.org/yihui/rmarkdown-cookbook/ |
| Code chunk options | Full list of options (lines that start with #|) you can use for Quarto documents, again with syntax modifications | https://yihui.org/knitr/options/ |
6.3 Next Steps in Code Reproducibility
- Version control : https://elixir-europe-training.github.io/ELIXIR-TrP-VersionControlR-CodeRep/
- Documentation: https://elixir-europe-training.github.io/ELIXIR-TrP-DocumentationR-CodeRep/
- Testing: https://elixir-europe-training.github.io/ELIXIR-TrP-TestingR-CodeRep/
- CI/CD: https://elixir-europe-training.github.io/ELIXIR-TrP-CICD-R-CodeRep/
- Containers: https://elixir-europe-training.github.io/ELIXIR-TrP-ContainersR-CodeRep/
6.4 Contributing to this course
This course has been developed via a colloboration of researchers, teachers and students. Found a typo? Something missing? Have a suggestion? We welcome further contributions and suggestions from everyone. If you would like to contribtue to course development, have a suggestion or just want more information, go here.