Introduction
Ulysses is an OHDSI R package serving as a workflow tool for the setup and organization of an RWE study. Ulysses draws inspiration from the R package usethis, which is a workflow tool used for the development of R packages, providing functions to automate the initialization of an R package and helpers for its maintenance. Similarly, RWE studies have a lot of documentation, code and results that need to be maintained and versioned. Organization of these components can be complicated without a strict organizational standard. The Ulysses study workflow tool is not specific to OMOP/OHDSI and can be used for other setups; it does provide automation focused on OHDSI/OMOP application.
Part of the Ulysses philosophy is contextualizing an RWE study/pipeline as a unit of software. As observational studies have become more and more popular given the access to longitudinal observational databases (such as claims and EHR) there is a lack of consistent standards on how code is maintained and executed. RWE studies have become more like software projects requiring a encapsulated root project with standard folders to source elements of the RWE pipeline such as inputs, functions, output and documentation to support these elements. A standard directory structure makes things more organized allowing for collaborative development and consistent execution based on a known structure.
The basic functions of Ulysses include:
- Implementation of standard directory structure - see Ulysses Stucture
- Launch of Ulysses style code repository - see Get Started
- Input Manifest helper functions
- Helpers to pull cohorts and concept sets from WebApi
- Git Helpers to initialize and sync repo
Technical Setup
Installation
See the instructions here for configuring your R environment, including RTools and Java.
In R, use the following commands to download and install Ulysses:
install.packages("remotes")
remotes::install_github("ohdsi/Ulysses")- Install quarto