Writing Reproducible Manuscripts in R and Python

Open Science practices are becoming central to the way research is conducted. In this workshop, you will learn to set up a reproducible workflow to create a publication-ready manuscript that combines data, R or Python code, text, and references.  

During this 3-hour workshop, you will use the Quarto publishing system in conjunction with R or Python - you can use the programming language you prefer. More specifically, you will learn how to: 

  • Create a reproducible project (folder) structure
  • Use Markdown syntax effectively for writing text
  • Run analyses in code chunks or cells
  • Manage references using Zotero and Better BibTex for Zotero
  • ‘Render’ your Quarto project to Word, HTML, and pdf files 

This workflow reduces the amount of human error, improves computational reproducibility and makes updating the manuscript more efficient. If time allows, we can also touch upon managing software dependencies, using Git and GitHub for version control, and publishing your project via Zenodo or Open Science Framework (OSF) to obtain a DOI. 

By the end of the workshop, you will be sufficiently familiar with the components of a reproducible manuscript and the tools required to create one, so you can implement the workflow in your own research projects.  

Note that this workshop focuses on the (reproducible) manuscript as a whole and it does not dive into the (analysis) code itself. The latter is addressed in our workshop on Best Practices in Writing Reproducible Code, which is aimed at participants with more experience in programming in R & Python. 

Prerequisites 

  • We recommend basic knowledge of R or Python to follow this workshop. You can gain this knowledge in our workshops Introduction to R and Data or Introduction to Python.
  • You do not need to bring your own research project to the workshop.
  • The workshop is open to participants from Utrecht University (UU) and UU-affiliated organizations (for example, UMC Utrecht) only.   

Costs 

There are no costs associated with this workshop.  

Planned dates 

The workshop is planned for the following dates:  

For more information on registration and location, please visit the agenda item for a workshop date. We reserve the right to cancel or reschedule workshops due to insufficient registrations or unforeseen circumstances. 

Credits

This workshop takes about 3 hours. Due to the short duration of this workshop, you cannot earn ECTS for attending. 

Contact

If you have any questions, please contact us via info.rdm@uu.nl. 

More information

Can’t make it to this workshop? Do you prefer to learn in a self-paced manner? Our course materials are available online! You can work through them at your own pace and drop by the Walk-In Hours and/or Programming Café if you have any questions.