Introduction
This software tool is designed to extract data from a randomized subset of individuals within a cohort and make it available for exploration in a ‘Shiny’ application environment. It retrieves date-stamped, event-level records from one or more data sources that represent patient data in the Observational Medical Outcomes Partnership (OMOP) data model format. This tool features a user-friendly interface that enables users to efficiently explore the extracted profiles, thereby facilitating applications, such as reviewing structured profiles. The output of this R-package is a self-contained R shiny that contains person-level data for review.
Warning
- Contains person level data. This package is not to be considered de-identified.
- Please do not share the output with others as it may violate protected health information.
- .RDS file in output contains PHI.
Features
- From an instantiated cohort, identifies specified number of random persons. It also allows for non random selection by specifying a set of personId as input.
- Extracts person level data for each person from the common data model, and constructs a results object in rds form. This rds object has person level data with personId and dates.
- Allows additional de-identification using two optional mechanisms (shift dates and replace OMOP personId with a new random id). Shift date: shifts all dates so that the first observation_period_start_date for a person is set to January 1st 2000, and all other dates are shifted in relation to this date. Also creates and replaces the source personId with a new randomly generated id.
- Creates a R shiny app in a specified local folder, that can then be published to a shiny server or explored locally.
- Allows navigation of patient event data using configurable parameters from within the shiny application, e.g. regular expression to filter event.
How to use
- The output of createCohortExplorerApp is a shiny App with person level data in .rds. It is in the output folder.
- Go the output location in your file browser (e.g. windows file explorer in a Windows computer) and start ‘CohortExplorer.Rproj’.
- Optionally, in R console now run renv::restore() to enable renv. This will download all required packages and dependencies and set up the run environment.
- Next call to shiny::runApp()
- If you want to run this shiny App on a remote Shiny Server, you may copy all the files in the output to the remote shiny servers new app file folder. run renv::restore() in the shiny server and restart app.
Installation
See the instructions here for configuring your R environment, including RTools and Java.
In R, use the following commands to download and install CohortExplorer:
install.packages("remotes")
remotes::install_github("ohdsi/CohortExplorer")User Documentation
Documentation can be found on the package website.
PDF versions of the documentation are also available: * Package manual: CohortExplorer.pdf
Support
- Developer questions/comments/feedback: OHDSI Forum
- We use the GitHub issue tracker for all bugs/issues/enhancements
Contributing
Read here how you can contribute to this package.