• The project example folder is a simplified version of the original project available at: https://osf.io/6mvq7. We kept only files that are used in the episodes to make it less confusing for learners to navigate multiple folders that won’t be used in the lesson. You are welcome to use the more complete version if you would like to show some additional examples. We advise instructors to use the main branch. The renv branch has the same content as the main branch, with the addition of having renv enabled for better reproducibility.
• All Episodes, whenever possible, emphasize using RStudio GUI features over R commands (e.g., install packages using GUI dialog) in order to minimize cognitive overload. Less for learners to remember, and they can always see commands echoed in the console.
• The workshop was designed to include a basic tour of RStudio and its features before introducing Quarto, allowing it to accommodate different audience levels. Depending on the audience, this part may be skipped.
• Ep. “Scientific reproducibility: What is it for?”: reiterate that having a Github account is required for this workshop. Any learners who have not yet signed up for a Github account should do so during the first break of the workshop.
• Ep. “Good Practices for Managing Projects in RStudio”: it might need to be clarified to all learners the distinction between the console and the terminal. So, we recommend that instructors cover this difference: “using the console, you submit commands to and interact with R through RStudio; whereas the terminal provides command line access to the computer’s operating system”.
• Ep. “Introduction to Working with Quarto documents”: when the option to produce pdf outputs using TinyTex is presented, as noted in the lesson instructors should clarify that it requires extra installation that is separate from the lesson. Instructors may choose to demonstrate the PDF on the side. If you choose so, make sure to install TinyTex following the same approach you used to install quarto (command line vs. console). If you installed quarto through the RStudio IDE, then quarto will only be on your path if you run the integrated RStudio IDE terminal
• Ep. “Getting your project set up with Version Control in RStudio”: when creating a project from GitHub, mention or quickly show that they also have the option to create a new project from scratch and set up a GitHub repository. If there is time, and depending on the entry knowledge level of the cohort, there could be some more explanation of the differences between these two.
• Ep. “Adding Code-Generated Plots and Figures”, DO NOT skip Challenge 2 “CHALLENGE 2: Add a caption to Figure 3”, Otherwise it will affect “Challenge 4: Adding cross-reference for code block figures” in Ep. “Bibliography, Citations & Cross-Referencing”.
• Ep. “Bibliography, Citations & Cross-Referencing”: Make sure to address that the YAML only contains bibliography: references.bib because the example paper contains citations. The visual model will automatically add this when the first citation is added. To connect a pre-existent reference.bib file and enter citations using keys, that needs to be manually added to the YAML. Remember that Zotero will only show for those with it installed on their computers. Also, some learners may experience issues with the DOI lookup feature. This seems to be a bug with the IDE, or some underlying unreliability of the services providing the DOIs. See open issue: https://github.com/rstudio/rstudio/issues/9863.
• Cheasheets to recommend: DataCamp and Rstudio - Quarto.