OHDSI/SelfControlledCohort

Name: SelfControlledCohort

Owner: Observational Health Data Sciences and Informatics

Description: 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.

Created: 2014-04-06 09:20:27.0

Updated: 2017-08-25 17:36:35.0

Pushed: 2017-11-08 15:00:59.0

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Size: 673

Language: R

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README

SelfControlledCohort

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

ary(SelfControlledCohort)

ectionDetails <- createConnectionDetails(dbms = "postgresql",
                                         user = "joe",
                                         password = "secret",
                                         server = "myserver")

esults <- runSelfControlledCohort(connectionDetails,
                                 cdmDatabaseSchema = "cdm_data",
                                 exposureIds = c(767410, 1314924, 907879),
                                 outcomeIds = 444382,
                                 outcomeTable = "condition_era")

ary(sccResults)

Technology

SelfControlledCohort is an R package.

System Requirements

Requires R. Libraries used in SelfControlledCohort require Java.

Dependencies

• DatabaseConnector
• SqlRender
• OhdsiRTools

Getting Started

1. The DatabaseConnector and SqlRender packages require Java. Java can be downloaded from http://www.java.com.

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

   all.packages("devtools")
   ary(devtools)
   all_github("ohdsi/OhdsiRTools") 
   all_github("ohdsi/SqlRender")
   all_github("ohdsi/DatabaseConnector")
   all_github("ohdsi/SelfControlledCohort")
   

Getting Involved

• Package manual: SelfControlledCohort.pdf
• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

License

SelfControlledCohort is licensed under Apache License 2.0

Development

SelfControlledCohort is being developed in R Studio.

Development status

Beta