Writing Reproducible Research Papers with R Markdown

Origin

This repository was forked from Resul Umit.

He created the materials for a workshop on writing reproducible research papers with R Markdown, first taught at Campus Luzern in March 2020.

Felix Golcher adapted for a workshop held for the CRC 1412 Register.

This material is published under CC-BY-SA 3.0. An easy to read summary of this permissive licence is available on the Creative Commons website.

Contents

The workshop is divided into ten parts. Most parts include exercises — 40+ in total.

Part 1. Getting the Tools Ready - e.g., downloading course material	Part 6. The R of Rmarkdown: Code Chunks and Inline Code - e.g., plotting data
Part 2. Introducing R Markdown - e.g., creating a new document	Part 7. Addressing Functionality Gaps - e.g., adjusting line spacing
Part 3. Setting Metadata - e.g., defining output format	Part 8. Using Version Control - e.g., integrating Git and GitHub
Part 4. Writing Text - e.g., adding emphasis to text	Part 9. Collaborating with Others - e.g., working simultaneously with co-authors
Part 5. Managing References - e.g., citing sources	Part 10. Working on a Real Project - e.g., converting a work-in-progress of yours

The parts

• Part A. Cache Functionality
  • don't recompute everything with every compilation
• Part B. Reusing Code
  • e.g., building up figures, child documents
• Part C. Fancy Templates
  • e.g., producing publication ready papers

are not yet produced. A exists as an idea only, there are exercises for B and C is essentially done by showing people the rticles package.

At the moment the parts are quite different in size.

I got through part 6 and a bit of Part B. in 3 days a 120 Minutes.

Exercise Branch

Exercises and solutions can be found in the exercises branch.

Files and directories.

Below are the workshop materials kept in this repository.

• presentation/rmd_workshop.Rmd: an R Markdown file behind the slides, produced with the xaringan package (Xie, 2020)
• presentation/data: containing some example data on journal statistics.
• presentation/image: static images used in the Rmd file.

References

Blair, G., Cooper, J., Coppock, A., Humphreys, M., Rudkin, A. and Fultz, N. (2019). fabricatr: Imagine your data before you collect it. R package, version 0.10.0.

Gagolewski, M. (2020). stringi: Character String Processing Facilities. R package, version 1.4.6.

Wiernik, B. M. (2020). American Psychological Association 7th edition (no ampersand). Citation style language file, version 1.0.

Xie, Y. (2020). xaringan: Presentation Ninja. R package, version 0.18.