Reproducible Reports with Quarto and R Markdown: A Short Course

A 3-Day Livestream Seminar Taught by Aaron Gullickson, Ph.D.

Download Sample Course Slides

Reproducible reports provide a means to combine the code that produces a data analysis with the actual document that reports on that analysis. For most researchers, the work of doing analysis and writing up a report or paper about that analysis are distinct parts of our workflow. This traditional approach has significant drawbacks due to the added labor of moving tables, figures, and numbers between media, the potential errors involved in transcription, and an overall lack of transparency. Reproducible reports eliminate this division in workflow and allow researchers to focus simultaneously on both the analysis and its interpretation by weaving together narrative and code in a single dynamic document.

The Quarto system is one of the most powerful ways to produce reproducible reports that combine narrative and code to write academic papers, professional-quality reports, lab notebooks, web pages, blogs, presentations, and more. Quarto is the successor to the popular R Markdown system, but also includes powerful new features and the ability to use a variety of coding languages such as R and Python. Based on the simple and lightweight markdown syntax, Quarto is easy to learn and use.

Quarto works natively with R, but can also be used with Python. This course will familiarize you with how Quarto works and the principles behind its design. The primary focus will be on producing research documents such as papers and reports using Quarto, but various output formats will also be introduced.

Starting March 16, we are offering this seminar as a 3-day synchronous*, livestream workshop held via the free video-conferencing software Zoom. Each day will consist of two lecture sessions which include hands-on exercises, separated by a 1-hour break. You are encouraged to join the lecture live, but will have the opportunity to view the recorded session later in the day if you are unable to attend at the scheduled time.

*We understand that finding time to participate in livestream courses can be difficult. If you prefer, you may take all or part of the course asynchronously. The video recordings will be made available within 24 hours of each session and will be accessible for four weeks after the seminar, meaning that you will get all of the class content and discussions even if you cannot participate synchronously. 

Closed captioning is available for all live and recorded sessions.

More Details About the Course Content

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.

Computing

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.

Who Should Register?

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.

Outline

Day 1: Understanding Quarto

  • Why should I use reproducible reports?
  • Create your first Quarto document
  • Learn the Quarto syntax
  • Understand the code chunk
  • How Quarto creates your document
  • Activity: Setup a Quarto document

Day 2: Writing Papers and Reports with Quarto

  • Use TinyTex for pdf output
  • Make beautiful figures in Quarto
  • Make complex tables in Quarto
  • Learn how to cross-reference tables and figures
  • Include citations and bibliographies
  • Activity: Create figures and tables in a Quarto document

Day 3: Quarto for Everything

  • Customize output with templates
  • Create dynamic output with parameterized reports
  • Make Quarto presentations
  • Make Quarto posters
  • Create web content with Quarto

Reviews of Reproducible Reports with Quarto and R Markdown

“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 R Markdown for, well, almost everything. Also, the instructor pointed the class towards online collaborative tools for co-working on and rendering 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 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

“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

Seminar Information

Thursday, March 16 –
Saturday, March 18, 2023

Daily Schedule: All sessions are held live via Zoom. All times are ET (New York time).

10:00am-12:30pm (convert to your local time)
1:30pm-3:30pm

Payment Information

The fee of $995 includes all course materials.

PayPal and all major credit cards are accepted.

Our Tax ID number is 26-4576270.