README.md

In CohortGenerator: Cohort Generation for the OMOP Common Data Model

CohortGenerator

CohortGenerator is part of HADES.

Introduction

This R package contains functions for generating cohorts 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.
• Provides functions for performing incremental tasks. This is used by CohortGenerator to skip any cohorts that were successfully generated in a previous run. This functionality is generic enough for other packages to use for performing their own incremental tasks.

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 3.6.0 or higher).

Getting Started

1. 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.

2. In R, use the following commands to download and install CohortGenerator:

   r 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
• 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

This package is being developed in RStudio.

Development status

Beta

CohortGenerator documentation built on Oct. 1, 2024, 1:09 a.m.