Summary and Setup

OMOP Carpentries Course.

This course should provide clinicians and analysts with an introduction to the OMOP Common Data Model and how they can use R to access data and answer clinical questions.

The course is intended to be run over two days in person, or to be self directed online.

We suggest that learners are familiar with R and the tidyverse or do one of the carpentries introductory R courses.

Prerequisite

A laptop with the current versions of the following installed:
- the R software itself, and
- RStudio Desktop.
Download workshop.zip.

Setup instructions

Install R Packages

install.packages(“dplyr”, verbose=FALSE)
install.packages(“readr”, verbose=FALSE)
install.packages(“purrr”, verbose=FALSE)
install.packages(“CDMConnector”, verbose=FALSE)
install.packages(“duckdb”, verbose=FALSE)
install.packages(“lubridate”, verbose=FALSE)
install.packages(“renv”, verbose=FALSE)
install.packages(“arrow”, verbose=FALSE)

Create environment

Make a new folder in your Desktop called omop_course.
Download workshop.zip and move the file to this folder.
If it’s not unzipped yet, unzip it. There should now be a folders called workshop in the omop_course folder containing sub folders code and data.
You can access this folder from the Unix shell with:

BASH

$ cd
$ cd Desktop/omop_course/workshop