IC Temporal Pattern Discovery

Introduction

This R package is an implementation of the IC Temporal Pattern Discovery method to estimate risk by combining a self-controlled and cohort design. It is designed to run against observational databases in the OMOP Common Data Model.

Features

• Extracts the necessary data from a database in OMOP Common Data Model format.
• Supports various risk and control window definitions.
• Create Chronographs to explore time-to-event relationships.

Example

library(SelfControlledCohort)

connectionDetails <- createConnectionDetails(dbms = "postgresql",
                                             user = "joe",
                                             password = "secret",
                                             server = "myserver")
                                             
exposureOutcomePairs = data.frame(outcomeId = c(196794, 196794, 312648), 
                                  exposurId = c(1501700, 1545958, 1551803))
                                   
ictpdData <- getDbIctpdData(connectionDetails, 
                            cdmDatabaseSchema = "cdm_schema.dbo", 
                            exposureOutcomePairs = exposureOutcomePairs)
                             
ictpdResults <- calculateStatisticsIC(ictpdData)
 
ictpdResults                                             

Technology

IcTemporalPatternDiscovery is an R package.

System Requirements

Requires R (version 3.1.0 or higher). Libraries used in this package require Java.

Dependencies

• ParallelLogger
• DatabaseConnector
• SqlRender

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 IcTemporalPatternDiscovery:

install.packages("devtools")
library(devtools)
install_github("ohdsi/ParallelLogger") 
install_github("ohdsi/IcTemporalPatternDiscovery") 

Getting Involved

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

License

IcTemporalPatternDiscovery is licensed under Apache License 2.0

Development

IcTemporalPatternDiscovery is being developed in R Studio.

Development status

Beta

Acknowledgements

This package was developed by Tomas Bergvall, adapted by Martijn Schuemie.