Cohort Incidence Analysis for the OMOP Common Data Model

Provides functionality for performing cohort incidence analyses against data stored in the OMOP Common Data Model (CDM). The package generates database-specific SQL, executes analyses across supported database platforms, and returns standardized incidence estimates using configurable time-at-risk, stratification, and cohort definitions. It is intended to support reproducible observational research within the OHDSI analytics framework.

CohortIncidence

CohortIncidence is part of HADES.

Introduction

An R package and Java library for calculating incidence rates on the OMOP CDM.

Features

• Handles specifications of T-O-TAR-Subgroup pairs, and performs the calculation on the cross-product of the elements.
• Specify clean windows to account for immortal time after outcome.
• Allows multiple exposure and multiple outcomes per person accounting for time at risk and clean window paramaters.

Technology

CohortIncidence is an R package which wraps a Java library that implements most of the functions of the package.

System Requirements

Requires R and Java.

Getting Started

R package

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

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

install.packages("remotes")
library(remotes)
install_github("ohdsi/CohortIncidence") 

Java library

The Java library is hosted in an OHDSI Nexus repo, so you only need to add the repository and dependnecy to your maven.xml file in order to use it in your own Java project.

1. First add the OHDSI Nexus repository so that maven can find and download the artifact automatically:

  <repositories>
    <repository>
      <id>ohdsi</id>
      <name>repo.ohdsi.org</name>
      <url>https://repo.ohdsi.org/nexus/content/groups/public</url>
    </repository>
  </repositories>

2: Include the CohortIncidence dependency in your pom.xml

<dependency>
	<groupId>org.ohdsi.sql</groupId>
	<artifactId>CohortIncidence</artifactId>
	<version>{latest version}</version>
</dependency>

User Documentation

Documentation can be found on the package website.

PDF versions of the documentation are also available:

• Vignette: Using CohortIncidence

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

CohortIncidence is licensed under Apache License 2.0

Development

CohortIncidence is being developed in R Studio.

Development status

Released, Under Active Development