Intermediate Reproducible Research in R
An intermediate workshop on modern approaches and workflows to processing data
Luke W. Johnston 
Anders Askeland
Welcome
Reproducibility and open scientific practices are increasingly demanded of, and needed by, scientists and researchers in our modern research environments. As our tools for generating data become more sophisticated and powerful, we also need to use more sophisticated and powerful tools for processing the data. Training on how to use these tools and how to build modern data processing skills is lacking for researchers, even though this work takes up a large amount of researchers’ time and is extremely time-consuming and technical. As a consequence of this lack of awareness for the need of these skills, how exactly data is processed is poorly, if at all, described in scientific studies. This hidden aspect of research could have major impacts on the reproducibility of studies. This workshop is therefore aimed to specifically start addressing these types of problems.
This 3-day long workshop is designed to do participatory live-typing, where the teacher demonstrates the tasks on their computer connected to a projector while learners type along on their own computer. The workshop also includes reading tasks, discussion activities, hands-on exercises, and a team project at the end. In all of these activities, we work with real-world (open) datasets.
This website contains all of the material for the workshop, including readings, exercises, presentations, live-typing material, and images. It is structured as a book, with “chapters” as sessions, in order of appearance. We make heavy use of the website throughout the workshop where “type-along” sessions almost identically follow the material on the website (with slight modifications for time or more detailed explanations).
Check out the overview section of the workshop, starting with the Syllabus (1 Syllabus).
If you plan on attending the workshop, please make sure to complete the Pre-workshop tasks (5 Overview) to get set up and ready for the workshop. The pre-workshop tasks include a survey that you need to fill out before the workshop starts.
Target audiences
This website and its content are targeted to three groups:
- For the learners to use during the workshop, both to follow along and also to use as a reference after the workshop ends. A more detailed description of who the learner is can be found in the Is this for you? section (2 Is this for you?).
- For the teachers to use as a guide for when they do the type-along sessions.
- For those who are interested in teaching, who may not have much experience or may not know where to start, to use this website as a guide to running and teaching their own workshops.
Re-use and licensing
The workshop material is licensed under the Creative Commons Attribution 4.0 License, so the material can be used, re-used, and modified, as long as there is attribution to this source. Check out the For teachers section (Appendix B — For teachers) for more details and tips on using this material for teaching.
Contributing
Want to contribute to this workshop? Look through our CONTRIBUTING page for contribution guidelines on how to get started.
Contributors
These are the people who have contributed by submitting changes through pull requests 🎉
@lwjohnst86, @signekb, @AndersAskeland, @MaleneRevsbech, @hchats, @LouiseEB, @StineScheuer, @krauthn
How the website is made
The workshop material is created using Quarto to write the material and create the book format, GitHub to host the Git repository of the material, and GitHub Actions with Netlify to build and host the website. The original source material for this workshop is found on the r-cubed-intermediate GitHub repository.
Acknowledgements
The workshop material draws inspiration from these excellent resources:
- R for Data Science
- Advanced R
- R Packages
- UofTCoders Reproducible Quantitative Methods for EEB
- Software and Data Carpentry workshop material
The Danish Diabetes and Endocrinology Academy hosted, organized, and sponsored this workshop many times. A huge thanks to them for their involvement, support, and sponsorship! Steno Diabetes Center Aarhus and Aarhus University employs Luke, who is the lead teacher and educational resource developer.
