Capr

Capr is part of HADES.

Cohort definition Application Programming in R

Introduction

Capr is an R package to develop and manipulate OHDSI cohort definitions. This package assists in creating a cohort definition that can be compiled by circe-be using CirceR. Cohort definitions developed in Capr are compatible with OHDSI ATLAS. Additionally the package allows for development of cohort design components, sub-items of a cohort design that are meant to be reusable and mutable to assist creating cohorts in study development.

System Requirements

Requires R (version 3.6.0 or higher). Installation on Windows requires RTools. Libraries used in Capr require Java. Capr requires a connection to an OMOP vocabulary database to query concepts.

Installation

1. See the instructions here for configuring your R environment, including RTools and Java.

2. In R, use the following commands to download and install Capr:

install.packages("remotes")
remotes::install_github("ohdsi/Capr")

3. Optionally, run this to check if Capr was correctly installed:

connectionDetails <- createConnectionDetails(dbms="postgresql",
                                             server="my_server.org",
                                             user = "joe",
                                             password = "super_secret")

checkCmInstallation(connectionDetails)

Where dbms, server, user, and password need to be changed to the settings for your database environment. Type

?createConnectionDetails

for more details on how to configure your database connection.

User Documentation

Documentation can be found on the package website.

PDF versions of the documentation are also available:

• Vignette: Capr Tutorial
• Vignette: Capr Complex Cohort Example
• Package manual: Capr.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.

License

Capr is licensed under Apache License 2.0

Development

Capr is being developed in R Studio.