This package is considered a duplicate. The official version of this package is found at:https://ohdsi.r-universe.dev/CohortGenerator

Package: CohortGenerator 1.1.0

Anthony Sena

CohortGenerator: Cohort Generation for the OMOP Common Data Model

Generate cohorts and subsets using an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database. Cohorts are defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).

Authors:Anthony Sena [aut, cre], Jamie Gilbert [aut], Gowtham Rao [aut], Freddy Avila Cruz [aut], Martijn Schuemie [aut], Observational Health Data Science and Informatics [cph]

CohortGenerator_1.1.0.tar.gz
CohortGenerator_1.1.0.tar.gz(r-4.7-any)CohortGenerator_1.1.0.tar.gz(r-4.6-any)
CohortGenerator_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CohortGenerator/json (API)
NEWS

# Install 'CohortGenerator' in R:

install.packages('CohortGenerator', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ohdsi/cohortgenerator/issues

Pkgdown/docs site:https://ohdsi.github.io

Uses libs:

openjdk– OpenJDK Java runtime, using Hotspot JIT

Datasets:

omopCdmDrugExposure - OMOP CDM Drug Exposure Sample Data
omopCdmPerson - OMOP CDM Person Sample Data

On CRAN:

openjdk

5.51 score 230 scripts 413 downloads 66 exports 55 dependencies

Last updated from:795a9afdfc. Checks:2 WARNING, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	WARNING	209
source / vignettes	OK	247
linux-release-x86_64	WARNING	199
wasm-release	OK	158

Exports:addCohortSubsetDefinition addCohortTemplateDefintion addExcludeOnIndexSubsetDefinition addIndicationSubsetDefinition addRestrictionSubsetDefinition addSqlCohortDefinition addUnionCohortDefinition checkAndFixCohortDefinitionSetDataTypes CohortSubsetDefinition CohortSubsetOperator CohortTemplateDefinition computeChecksum computeCohortAttrition createAtcCohortTemplateDefinition createCohortSubset createCohortSubsetDefinition createCohortSubsetOperator createCohortTables createCohortTemplateDefintion createDemographicSubset createDemographicSubsetOperator createEmptyCohortDefinitionSet createEmptyNegativeControlOutcomeCohortSet createLimitSubset createLimitSubsetOperator createResultsDataModel createRxNormCohortTemplateDefinition createSnomedCohortTemplateDefinition createSubsetCohortWindow createUnionCohortTemplate DemographicSubsetOperator dropCohortStatsTables exportCohortStatsTables exportCohortSubsetStatsTables generateCohortSet generateNegativeControlOutcomeCohorts getCohortCounts getCohortDefinitionSet getCohortInclusionRules getCohortStats getCohortTableNames getCohortValidationCounts getDataMigrator getExcludeOnIndexSubsetDefinitionIds getIndicationSubsetDefinitionIds getLastGeneratedCohortChecksums getRestrictionSubsetDefinitionIds getResultsDataModelSpecifications getSubsetDefinitions getTemplateDefinitions insertInclusionRuleNames isCamelCase isCohortDefinitionSet isFormattedForDatabaseUpload isSnakeCase LimitSubsetOperator migrateDataModel readCsv runCohortGeneration sampleCohortDefinitionSet saveCohortDefinitionSet saveCohortSubsetDefinition SubsetCohortWindow SubsetOperator uploadResults writeCsv

Dependencies:backports bit bit64 blob checkmate cli clipr cpp11 crayon DatabaseConnector DBI dbplyr digest dplyr fastmap generics glue hms jsonlite later lifecycle lubridate magrittr memuse ParallelLogger pillar pkgconfig pool prettyunits progress purrr R6 Rcpp readr ResultModelManager rJava rlang rstudioapi snow SqlRender stringi stringr tibble tidyr tidyselect timechange triebeard tzdb urltools utf8 vctrs vroom withr xml2 zip

Creating Cohort Subset Definitions

James P. Gilbert, Freddy Avila Cruz and Anthony G. Sena

Rendered fromCreatingCohortSubsetDefinitions.Rmdusingknitr::rmarkdownon Jun 01 2026.

Last update: 2026-02-10
Started: 2024-09-16

Generating Cohorts

Anthony G. Sena and Martijn J. Schuemie

Rendered fromGeneratingCohorts.Rmdusingknitr::rmarkdownon Jun 01 2026.

Last update: 2026-02-10
Started: 2024-09-16

Sampling Cohorts

James P. Gilbert

Rendered fromSamplingCohorts.Rmdusingknitr::rmarkdownon Jun 01 2026.

Last update: 2025-11-12
Started: 2024-09-16

Using Template Cohorts

James P. Gilbert

Rendered fromUsingTemplateCohorts.Rmdusingknitr::rmarkdownon Jun 01 2026.

Last update: 2026-02-10
Started: 2025-11-12

Citation

Readme and manuals

Help Manual

Help page	Topics
Add cohort subset definition to a cohort definition set	addCohortSubsetDefinition
Add Cohort template definition to cohort set	addCohortTemplateDefintion
Add exclude on index subset definition	addExcludeOnIndexSubsetDefinition
Add Indication Subset Definition	addIndicationSubsetDefinition
Add Restriction Subset Definition	addRestrictionSubsetDefinition
Add an sql cohort definition	addSqlCohortDefinition
Add union cohort definition to cohort definition set	addUnionCohortDefinition
Check if a cohort definition set is using the proper data types	checkAndFixCohortDefinitionSetDataTypes
Cohort Subset Definition	CohortSubsetDefinition
Cohort Subset Operator	CohortSubsetOperator
Class for automating the creation of bulk cohorts	CohortTemplateDefinition
Computes the checksum for a value	computeChecksum
Compute cohort attrition from inclusion rule statistics	computeCohortAttrition
Create ATC Cohort Template Definition	createAtcCohortTemplateDefinition
Create Cohort Subset Operator	createCohortSubset
Create Subset Definition	createCohortSubsetDefinition
A definition of subset functions to be applied to a set of cohorts	createCohortSubsetOperator
Create cohort tables	createCohortTables
Create Cohort Template Definition	createCohortTemplateDefintion
Create Demographic Subset Operator	createDemographicSubset
Create createDemographicSubset Subset operator	createDemographicSubsetOperator
Create an empty cohort definition set	createEmptyCohortDefinitionSet
Create an empty negative control outcome cohort set	createEmptyNegativeControlOutcomeCohortSet
Create Limit Subset Operator	createLimitSubset
Create Limit Subset Operator	createLimitSubsetOperator
Create the results data model tables on a database server.	createResultsDataModel
Create Rx Norm Cohort Template Definition	createRxNormCohortTemplateDefinition
Create SNOMED Cohort Template Definition	createSnomedCohortTemplateDefinition
Create a relative time window for cohort subset operations	createSubsetCohortWindow
Create cohort template to union multiple cohorts	createUnionCohortTemplate
Demographic Subset Operator	DemographicSubsetOperator
Drop cohort statistics tables	dropCohortStatsTables
Export the cohort statistics tables to the file system	exportCohortStatsTables
Export cohort subset statistics tables to the file system	exportCohortSubsetStatsTables
Generate a set of cohorts	generateCohortSet
Generate a set of negative control outcome cohorts	generateNegativeControlOutcomeCohorts
Count the cohort(s)	getCohortCounts
Get a cohort definition set	getCohortDefinitionSet
Get Cohort Inclusion Rules from a cohort definition set	getCohortInclusionRules
Get Cohort Inclusion Stats Table Data	getCohortStats
Used to get a list of cohort table names to use when creating the cohort tables	getCohortTableNames
Validate cohort	getCohortValidationCounts
Get database migrations instance	getDataMigrator
Get Exclude On Index Subset Definition Ids	getExcludeOnIndexSubsetDefinitionIds
Get Indication Subset Definition Ids	getIndicationSubsetDefinitionIds
Get last generated cohort checksums	getLastGeneratedCohortChecksums
Get Restriction Subset Definition Ids	getRestrictionSubsetDefinitionIds
Get specifications for CohortGenerator results data model	getResultsDataModelSpecifications
Get cohort subset definitions from a cohort definition set	getSubsetDefinitions
Extract template definitions from a cohort definition set	getTemplateDefinitions
Used to insert the inclusion rule names from a cohort definition set when generating cohorts that include cohort statistics	insertInclusionRuleNames
Used to check if a string is in lower camel case	isCamelCase
Is the data.frame a cohort definition set?	isCohortDefinitionSet
Is the data.frame formatted for uploading to a database?	isFormattedForDatabaseUpload
Used to check if a string is in snake case	isSnakeCase
Limit Subset Operator	LimitSubsetOperator
Migrate Data model	migrateDataModel
OMOP CDM Drug Exposure Sample Data	omopCdmDrugExposure
OMOP CDM Person Sample Data	omopCdmPerson
Used to read a .csv file	readCsv
Run a cohort generation and export results	runCohortGeneration
Sample Cohort Definition Set	sampleCohortDefinitionSet
Save the cohort definition set to the file system	saveCohortDefinitionSet
Save cohort subset definitions to json	saveCohortSubsetDefinition
Time Window For Cohort Subset Operator	SubsetCohortWindow
Abstract base class for subsets.	SubsetOperator
Upload results to the database server.	uploadResults
Used to write a .csv file	writeCsv