CohortGenerator
CohortGenerator is part of HADES.
Introduction
This R package contains functions for generating cohorts and cohort subsets using data in the CDM.
Features
- Create a cohort table and generate cohorts against an OMOP CDM.
- Get the count of subjects and events in a cohort.
- Define subsets of cohorts using different criteria or other cohorts.
- Create cohorts using templated SQL.
Example
# First construct a cohort definition set: an empty
# data frame with the cohorts to generate
cohortsToCreate <- CohortGenerator::createEmptyCohortDefinitionSet()
# Fill the cohort set using cohorts included in this
# package as an example
cohortJsonFiles <- list.files(path = system.file("testdata/name/cohorts", package = "CohortGenerator"), full.names = TRUE)
for (i in 1:length(cohortJsonFiles)) {
cohortJsonFileName <- cohortJsonFiles[i]
cohortName <- tools::file_path_sans_ext(basename(cohortJsonFileName))
# Here we read in the JSON in order to create the SQL
# using [CirceR](https://ohdsi.github.io/CirceR/)
# If you have your JSON and SQL stored differenly, you can
# modify this to read your JSON/SQL files however you require
cohortJson <- readChar(cohortJsonFileName, file.info(cohortJsonFileName)$size)
cohortExpression <- CirceR::cohortExpressionFromJson(cohortJson)
cohortSql <- CirceR::buildCohortQuery(cohortExpression, options = CirceR::createGenerateOptions(generateStats = FALSE))
cohortsToCreate <- rbind(cohortsToCreate, data.frame(cohortId = i,
cohortName = cohortName,
sql = cohortSql,
stringsAsFactors = FALSE))
}
# Generate the cohort set against Eunomia.
# cohortsGenerated contains a list of the cohortIds
# successfully generated against the CDM
connectionDetails <- Eunomia::getEunomiaConnectionDetails()
# Create the cohort tables to hold the cohort generation results
cohortTableNames <- CohortGenerator::getCohortTableNames(cohortTable = "my_cohort_table")
CohortGenerator::createCohortTables(connectionDetails = connectionDetails,
cohortDatabaseSchema = "main",
cohortTableNames = cohortTableNames)
# Generate the cohorts
cohortsGenerated <- CohortGenerator::generateCohortSet(connectionDetails = connectionDetails,
cdmDatabaseSchema = "main",
cohortDatabaseSchema = "main",
cohortTableNames = cohortTableNames,
cohortDefinitionSet = cohortsToCreate)
# Get the cohort counts
cohortCounts <- CohortGenerator::getCohortCounts(connectionDetails = connectionDetails,
cohortDatabaseSchema = "main",
cohortTable = cohortTableNames$cohortTable)
print(cohortCounts)Technology
CohortGenerator is an R package.
System requirements
Requires R (version 4.1.0 or higher).
Getting Started
Make sure your R environment is properly configured. This means that Java must be installed. See these instructions for how to configure your R environment.
In R, use the following commands to download and install CohortGenerator:
remotes::install_github("OHDSI/CohortGenerator")
User Documentation
Documentation can be found on the package website.
PDF versions of the documentation are also available:
- Vignette: Generating Cohorts
- Vignette: Creating Cohort Subset Definitions
- Vignette: Using Template Cohorts
- Package manual: CohortGenerator.pdf
Support
- Developer questions/comments/feedback: OHDSI Forum
- We use the GitHub issue tracker for all bugs/issues/enhancements
Contributing
Read here how you can contribute to this package.
License
CohortGenerator is licensed under Apache License 2.0
Development
CohortGenerator is being developed in RStudio.
Development status
CohortGenerator is actively being used in several studies and is ready for use.