Reproducible Reports with Quarto and R Markdown: A Short Course

The course will introduce you to the Quarto system and how you can use it to make fantastic-looking final products for your data analysis. You will learn the basic syntax of Quarto and how to create code chunks to insert executable code into your document. You will also learn how the basic structure of Quarto works to produce documents of various types. You will leave the course with an understanding of how to integrate tables, figures, and citations into a document to produce a professional-looking report or paper, as well as additional knowledge of how to apply the Quarto approach to other output formats such as presentations, posters, and web content.

The seminar will be very hands on. If you have a project that you would like to develop using Quarto, you are more than welcome to bring that to class with you.

Quarto is designed to work with the R programming language and works best when using the RStudio integrated development environment. You should download and install both R and RStudio on your local machine. Both of these applications are free, open-source, and available on major computing platforms.

If you’d like to take this course but are concerned that you don’t know enough R, there are excellent on-line resources for learning the basics. Here are our recommendations.

This course is for anyone who wants to learn how to use reproducible reports to simplify their workflow and improve their data analysis practices. Some familiarity with R is beneficial for the class, although the focus of the course will be on Quarto itself rather than the code that we write. So, if you are still a novice R user wanting to learn more, this class is for you. Quarto can also run Python, so if your work is primarily in Python, the class will also be of benefit.

Day 1: Understanding Quarto

• What are reproducible reports?
• Making your first Quarto document
• Understanding the Quarto rendering process
• Learning the Markdown syntax
• Adding executable code chunks

Day 2: Putting together a full report

• Creating beautiful figures in Quarto
• Making customized tables in Quarto
• Inserting citations
• Adding notations
• Cross-referencing everything

Day 3: Extending Quarto

• Using Quarto extensions
• Customizing appearance
• Making presentations
• Putting together a Quarto project
• Publishing your content online

“The course “Reproducible Reports with Quarto and R Markdown”, taught by Aaron Gullickson, surpassed all my expectations, and the teacher’s style was nothing short of exceptional. Throughout the duration of the course, I was continually impressed by his deep knowledge of the subject and his easy way of navigating complex concepts clearly and engagingly. I look forward to applying the valuable knowledge and skills I gained from his course in my cardiovascular research.”
  Elena Blasco-Colmenares, Johns Hopkins University

“This course was very thorough in exploring all of the uses of Quarto. The instructor, Dr. Gullickson, showed examples and gave us opportunities to play with the code. Dr. Gullickson also provided other resources that are helpful.”
  Colin Weidig, Reinvestment Fund

“The instructor was patient, kind, well-prepared, and very knowledgeable. His enthusiasm for the subject matter was completely contagious, and he really opened my eyes to the possibilities of using [Quarto and] R Markdown for, well, almost everything. Also, the instructor pointed the class towards online collaborative tools for co-working on and rendering [Quarto and] R Markdown documents, which I absolutely plan to incorporate into my own workflows.”
  Jessica Louise Ray, NORCE Norwegian Research Centre AS

“I think the instructor is a friendly, accessible guy with a ton of experience working with R and [Quarto and] R Markdown. This is my sixth or seventh SH course and overall, I think it’s the best place to learn advanced methods. This course did not change my mind. The overall quality of SH courses is very high.”
  James Swartz, University of Illinois Chicago

“I appreciated the practicality of the course. This is the best course I have taken in years!” 
  Alain Koffi, Johns Hopkins University 

“Good notes and explanation. The slides are also fun to look at as there is some nice humour in some of the pictures.”
  Yalini Easvaralingam, Monash University, Malaysia

“I think Aaron was very pedagogical and good at answering questions, and I also really appreciate the slides and generous sharing of example code (on GitHub, etc.).”
  Ulf Hammar, Uppsala University

“I liked the detailed demonstrations of the granular details of Quarto.”
  Soundarya Soundararajan