Creating Reproducible Reports with R Markdown: A Short Course

A 4-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.

One of the most popular ways to produce reproducible reports is R Markdown, which can be used to combine narrative and code to write academic papers, professional-quality reports, lab notebooks, web pages, blogs, presentations, and more. Using the simple and lightweight markdown system, R Markdown is easy to learn and use.

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

Starting June 7, we are offering this seminar as a 4-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. Participants are encouraged to join the lecture live, but will have the opportunity to view the recorded session later in the day if they are unable to attend at the scheduled time

*We understand that scheduling is difficult during this unpredictable time . 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.

More Details About the Course Content

The course will introduce you to the R Markdown system and how you can use it to make fantastic-looking final products for your data analysis. You will learn the basic syntax of R Markdown and how to create code chunks to insert executable code into your document. You will also learn how the basic structure of R Markdown 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 R Markdown 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 R Markdown, you are more than welcome to bring that to class with you.


R Markdown 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 R Markdown 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. R Markdown can also run Python, so if your work is primarily in Python, the class will also be of benefit.


Understanding R Markdown

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

Writing Papers and Reports with R Markdown

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

R Markdown for Everything

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

Seminar information

Tuesday, June 7, 2022 –
Friday, June 10, 2022

Each day will follow this schedule:

10:30am-12:30pm ET (New York time): Live session via Zoom

1:30pm-3:00pm ET: Live session via Zoom

Payment Information

The fee of $895 includes all course materials.

PayPal and all major credit cards are accepted.

Our Tax ID number is 26-4576270.