Do you work with clinical data taken from CHOP’s clinical data warehouse? Do you get data from the Clinical Reporting Unit (CRU)? If so, you might have struggled with how to prepare this data for analysis. Perhaps you aren’t sure how to prune the data and combine several tables into a single data source, or you’re frustrated with dealing with multiple rows per patient. How come you can’t get data that’s ready to just drop into a statistical program or hand over to a statistician?
To understand why the data looks the way it does, I suggest a quick read of Getting to One Row.
To learn how to work with this rich, raw data in R, we’ve created a new training course using swirl, which is a method of delivering training within R (preferably in RStudio, to enjoy all the assistance of this great development environment). There are many courses in swirl, covering different skills and areas of interest. With the development of Clinical Data in R, Arcus has joined the educational community with our first public swirl course.
To install swirl, enter the command
To load swirl into your working environment, type
Once you have swirl installed and loaded, if you’re brand new to R, it might make sense to install one of the basic courses that get you accustomed to working in R. For example, type
library(swirl) and then
install_from_swirl("R Programming"). There are other great swirl courses out there that you can check out at the swirl course repository.
Ready to learn how to work with clinical data, using swirl? Then type
install_course_github("arcus", "Clinical_Data_in_R"). This is the Arcus swirl course that is tailored to the CHOP investigator who uses data from CHOP’s EHR and needs to clean, combine, and analyze clinical data in R.
Once you’ve got a course (or two!) installed, type
swirl() to begin. The prompts can be a little silly (“You’re doing great!”), but the skills you’ll learn are worth the time and effort of going through swirl-based training. Have some ideas for other swirl courses? Email Arcus Education!