This is the GitHub repository for the workshop called Introduction to R for Clinical Data, given at the Children's Hospital of Philadelphia (CHOP) by Arcus Education and the CHOP R User Group.
Looking to learn this content? Check out the section on how to sign up for a workshop, and how to review material from previous workshops.
This repository contains the files you need to be able to complete the exercises in the workshop. Exercises for you to complete are in the exercises folder, and working solutions files are found in solutions.
This workshop is aimed at people who have never used R or RStudio and is appropriate for brand new beginners. In it, you'll learn the basics of R, RStudio / Posit, and Quarto / R Markdown. You'll work with fabricated clinical data and learn to ingest, visualize, reshape, and communicate findings, all using the R language.
Not interested in clinical data? If you work with any kind of tabular (table-shaped, with rows and columns) data, like data in spreadsheets, you might find this workshop useful.
This workshop is free and does not require any paid software. You will need a computer and a robust internet connection, however.
Before the workshop, please do the following.
Necessary:
Highly Recommended:
On the day of the workshop, we suggest the following:
The easiest way to do the workshop exercises is to create a free account at https://posit.cloud and then go to our workshop project and make your own permanent copy of this project so you can make changes and work with it later.
Alternately, in Posit Cloud you can also add a new project and select "New Project from Git Repository" and enter the url of this repository, namely https://github.com/arcus/intro-to-r-for-clinical-data.
If you want, you can install R and RStudio Desktop for free on your computer, following the instructions Posit offers. Then you can either:
The files here depend on several R libraries, which you can install using the following command:
install.packages(c(
"tidyverse",
"rmarkdown",
"flexdashboard",
"plotly",
"DT"
))Slides of the teaching presentation that accompany the workshop are available and you are welcome to follow along or refer back to them at a later date. The source code for these slides is included in the directory quarto_slides in this repository.
This workshop was last offered in December 2023. If you want to be notified when the next workshop gets scheduled sign up for the CHOP R User Group.
You can watch a recording of the August 2023 session of this workshop.
Much of the material from this workshop has also been adapted into interactive online tutorials you can work through at your own pace. We recommend the following sequence to learn the same content that is generally covered in this workshop:
All of the material in this GitHub repository is copyrighted under the Creative Commons BY-SA 4.0 copyright to make the material easy to reuse. We encourage you to reuse it and adapt it for your own teaching as you like!
Much of the material here owes its existence to Stephan Kadauke, MD, PhD, with important updates undertaken by other members of CHOP's R User Group. This is a collaborative effort and we are grateful to all who have contributed to these materials. This group includes Arcus Education, a CHOP group of data science educators, which is made up of:
We are also indebted to the dozens of people who have served as presenters, behind-the-scenes coordinators, TAs, and to the hundreds who have been our students. Without you, this workshop would not exist.