Introduction to Reproducible Publications with Quarto

This workshop explores the powerful combination of Quarto and RStudio to author scientific publications. Our aim is to enhance researchers’ adoption of open and reproducible practices while improving their project and data management skills. This workshop is structured into three modules. The modular format encourages instructors to view the workshop as a comprehensive but flexible curriculum, allowing them to focus on specific areas of interest. Recognizing variations in proficiency levels and familiarity with RStudio among learners, we have designed this workshop to be flexible, allowing for the abbreviation or skipping of episodes to cater to specific needs:

Module 1 - Reproducibility and Project Organization: This module consists of two episodes introducing learners to reproducible research and project management fundamentals. It lays the groundwork for a robust and transparent workflow, ensuring that all participants, whether beginners or those seeking a refresher, are on the same page before delving into the specifics of Quarto and RStudio Posit.

Module 2 - Quarto and RStudio: This module focuses on Quarto and its features for creating dynamic and reproducible documents. We guide learners through the ins and outs of Quarto, helping them harness this authoring framework and tool potential to create visually appealing, easily reproducible, and shareable documents.

Module 3 - Collaboration: This module shifts the focus to collaboration and publishing. It explores effective collaboration with others, using version control within RStudio, pushing local changes to a remote repository, managing dependencies for R/Quarto projects, and sharing reproducible research with a wider audience.

Prerequisites:

Experience in R/RStudio is recommended but not required. Experience, if not familiarity, with using your Unix Shell Terminal, and Version Control with Git is required. You will need a GitHub Account to fork and pull the example repo.

Schedule

		Setup	Download files required for the lesson
Day 1	00:00	1. Scientific reproducibility: What is it for?	What is reproducible research? How can RStudio help research to be more reproducible? What are the benefits of using RStudio for writing academic essays and papers?
	00:10	2. Good Practices for Managing Projects in RStudio	What are good research project management practices? What is an R Project file? How do you start a new R Project or open an existing one? How do you use version control to keep track of your work?
	00:40	3. Navigating RStudio and Quarto Documents	How do you find your way around RStudio? How do you start a Quarto document in Rstudio? How is a Quarto document configured, and how do I work with it?
	01:00	4. Working with projects in RStudio	How do I start or continue a project with Git versioning? What are the features in the RStudio Interface for working with Git? What are the basics of the Git versioning workflow?
	01:30	5. Introduction to Working with Quarto documents	What is Quarto? What is the breakdown of a Quarto document? How can you render the input file to the specified output format?
	01:55	6. Writing and Styling Qmd Documents	What is the Visual Editor in RStudio? Which features does the Visual Editor have? How can I can apply styling and formatting to Qmd documents in Rstudio more easily? How to add inline code?
	02:15	7. Adding Code to Quarto Documents	What is Knitr and how it works? What are code chunks, and how are they structured? How do you add and run code chunks? How can I avoid issues with relative paths?
	02:45	Finish
Day 2	00:00	8. Rendering & Customizing Code Outputs	How do you render code in Quarto documents? How do you apply code chunk options at the document level to customize your code? How do you label and caption code chunks? What is inline code and when should it be used?
	00:30	9. Advanced Code Chunk Options	How do you apply global options at the project level? How do you globally load data and packages? How do you run code from an external script in a code chunk? How do I run external scripts in a Quarto document?
	00:50	10. Bibliography, Citations & Cross-Referencing	How can you insert citations to your manuscripts using RStudio’s visual editor? How can you change citation styles? What are the options to display cited and uncited bibliography? How can you cross-reference content?
	01:25	11. Using Git in RStudio	How do I use version control in RStudio? How do I track and commit changes?
	01:40	12. Collaborating via GitHub	How do I authenticate with GitHub? How do I put my project on GitHub? How do I "push" my latest changes to GitHub?
	02:15	13. Managing Dependencies in R/RStudio	How can I avoid the dependency hell problem and make my code reproducible in the future? How can I document my computational environment? How can I manage package and software dependencies in RStudio?
	02:35	14. Publishing your project	What are the options for you to publish your project? What free and open publishing resources are available? What aspects should guide your choice? How can you create qmd documents using journal templates?
	02:45	15. Creating and sharing reproducible environments with renv	How can I manage package and software dependencies in RStudio? What is the renv package and how it works?
	03:15	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.