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An R package for performing self-controlled cohort analyses, a method to estimate risk by comparing time exposed with time unexposed among the exposed cohort.

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OHDSI/SelfControlledCohort

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SelfControlledCohort

Build Status codecov.io

SelfControlledCohort is part of HADES.

Introduction

This package provides a method to estimate risk by comparing time exposed with time unexposed among the exposed cohort.

Features

  • Extracts the necessary data from a database in OMOP Common Data Model format.
  • Supports stratification by age, gender, and index year.

Example

library(SelfControlledCohort)

connectionDetails <- createConnectionDetails(dbms = "postgresql",
                                             user = "joe",
                                             password = "secret",
                                             server = "myserver")
                                             
sccResults <- runSelfControlledCohort(connectionDetails,
                                     cdmDatabaseSchema = "cdm_data",
                                     exposureIds = c(767410, 1314924, 907879),
                                     outcomeIds = 444382,
                                     outcomeTable = "condition_era")

summary(sccResults)

Technology

SelfControlledCohort is an R package.

System Requirements

Requires R. Libraries used in SelfControlledCohort require Java.

Getting Started

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

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

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

User Documentation

Documentation can be found on the package website.

PDF versions of the documentation are also available:

Support

Contributing

Read here how you can contribute to this package.

License

SelfControlledCohort is licensed under Apache License 2.0

Development

SelfControlledCohort is being developed in R Studio.

Development status

Beta

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An R package for performing self-controlled cohort analyses, a method to estimate risk by comparing time exposed with time unexposed among the exposed cohort.

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