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R Markdown for Medicine:
From Data to Manuscript

R/Medicine 2019 conference

🗓️ September 30, 2019
🕗 09:00am - 05:00pm
📍 Canberra, Australia

Time Activity
09:00 - 10:30 Session 1 (R Markdown Basics)
10:30 - 11:00 Break 🍵
11:00 - 12:30 Session 2 (Advanced R Markdown)
12:30 - 01:30 Lunch 🍱
01:30 - 03:00 Session 3 (Templates)
03:00 - 03:30 Break 🍵
03:30 - 05:00 Session 4 (Collections)


In this full-day workshop, you’ll learn how to get more out of R Markdown (and friends). We will demystify how R Markdown works under the hood. You will learn practical tools and workflows to increase your efficiency and productivity using R Markdown (including RStudio IDE features and templates), while learning how to use some extension packages along the way. We assume that you have knit an R Markdown document before, but you don’t need to be an advanced R Markdown user to take this workshop.


Alison Hill is a Data Scientist & Professional Educator at RStudio. She received her PhD in psychology and quantitative methods from Vanderbilt University in 2008. Prior to joining RStudio, she was an Assistant Professor at Arizona State University, and an Associate Professor at Oregon Health & Science University (OHSU). Alison is one of the keynote speakers at the 2019 Young Statisticians Conference. She regularly leads workshops and develops online learning materials on topics like reproducible research, machine learning, and data visualization. She is also a co-author of the book ‘blogdown: Creating Websites with R Markdown’ ( Alison lives in Portland, Oregon with her husband and young daughter.


Welcome to the Communicating with R Markdown workshop! We look forward to meeting you in person. Before attending the workshop, please complete the following prework:

  1. Sign up for a free RStudio Cloud account at before the workshop. I recommend logging in with an existing Google or GitHub account, if you have one (rather than creating a new account with another password you have to remember).

  2. We will be using GitHub in this workshop for version control and publishing. Sign up for a free account at if you don’t already have one. Also:

  3. Complete this 10-minute interactive tutorial on Markdown.

  4. Please bring a laptop that has the following installed:

    • A recent version of R (>=3.6.0), which is available for free at

    • A recent version of RStudio Desktop (>=1.2), available for free (RStudio Desktop Open Source License)

    • The R packages we will use, which you can install by connecting to the internet, opening RStudio, and running at the command line:

      install.packages(c("rmarkdown", "devtools", "usethis", "here", 
                         "tidyverse", "xaringan", "flexdashboard", 
                         "distill", "bookdown", "blogdown"))
  5. Don’t forget your power cord!

On the day of the workshop, I’ll provide you with an RStudio Cloud project that contains all of the course materials. We will use the software listed above only as an important backup should there be problems with the on-site internet connection.

View slides (note: these slides are intentionally a loop and will play on autoadvance)

This work is licensed under a Creative Commons Attribution 4.0 International License.