An R package for performing the IC Temporal Pattern Discovery method.
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README.md

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

License

IcTemporalPatternDiscovery is licensed under Apache License 2.0

Development

IcTemporalPatternDiscovery is being developed in R Studio.

Development status

Build Status

Beta

Acknowledgements

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