OHDSI/IcTemporalPatternDiscovery

Name: IcTemporalPatternDiscovery

Owner: Observational Health Data Sciences and Informatics

Description: An R package for performing the IC Temporal Pattern Discovery method.

Created: 2014-12-22 23:33:26.0

Updated: 2017-04-13 08:34:09.0

Pushed: 2017-07-05 05:14:47.0

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Size: 320

Language: R

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README

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

Example

ary(SelfControlledCohort)

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

sureOutcomePairs = data.frame(outcomeId = c(196794, 196794, 312648), 
                              exposurId = c(1501700, 1545958, 1551803))

dData <- getDbIctpdData(connectionDetails, 
                        cdmDatabaseSchema = "cdm_schema.dbo", 
                        exposureOutcomePairs = exposureOutcomePairs)

dResults <- calculateStatisticsIC(ictpdData)

dResults                                             

Technology

IcTemporalPatternDiscovery is an R package.

System Requirements

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

Dependencies

• OhdsiRTools
• 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:

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

Alpha

Acknowledgements

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