This is the repository for the OHDSI study "Endometriosis Phenotype Characterization Across Observational Health Databases".
In this study we want to assess the prevalence of signs and symptoms, treatments, and healthcare utilization patterns among endometriosis patients at the time of diagnosis and relate these patterns to a comparison cohort of reproductive age women. The data for this work is observational health databases in the OMOP common data model.
To run this study please refer to the methods section in the study protocol. The protocol is in the documents folder in this repository.
Running this study requires the following:
- OMOP cdm version 5
- The use of R
- Access of the following tables: COHORT, DRUG_EXPOSURE, CONDITION_OCCURRENCE, VISIT_OCCURRENCE
- Results submission of .csv files to Noemie Elhadad noemie.elhadad@columbia.edu
How to run:
- Set your database, server, port, user & password, this example assumes you have set your environment variables to the requried values.
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = Sys.getenv("dbms"), server = Sys.getenv("server"), port = as.numeric(Sys.getenv("port")), user = Sys.getEnv("username"), password = Sys.getEnv("password")
- Run the package to create the cohorts
library(createCohorts)
- Run the package to generate the prevalence counts and output to study files.
library(main)