CohortGenerator1.0.2 package

Cohort Generation for the OMOP Common Data Model

addCohortSubsetDefinition

Add cohort subset definition to a cohort definition set

addCohortTemplateDefintion

Add Cohort template definition to cohort set

addExcludeOnIndexSubsetDefinition

Add exclude on index subset definition

addIndicationSubsetDefinition

Add Indication Subset Definition

addRestrictionSubsetDefinition

Add Restriction Subset Definition

addSqlCohortDefinition

Add an sql cohort definition

addUnionCohortDefinition

Add union cohort definition to cohort definition set

checkAndFixCohortDefinitionSetDataTypes

Check if a cohort definition set is using the proper data types

CohortGenerator-package

CohortGenerator: Cohort Generation for the OMOP Common Data Model

CohortSubsetDefinition

Cohort Subset Definition

CohortSubsetOperator

Cohort Subset Operator

CohortTemplateDefinition

Class for automating the creation of bulk cohorts

computeChecksum

Computes the checksum for a value

createAtcCohortTemplateDefinition

Create ATC Cohort Template Definition

createCohortSubset

Create Cohort Subset Operator

createCohortSubsetDefinition

Create Subset Definition

createCohortSubsetOperator

A definition of subset functions to be applied to a set of cohorts

createCohortTables

Create cohort tables

createCohortTemplateDefintion

Create Cohort Template Definition

createDemographicSubset

Create Demographic Subset Operator

createDemographicSubsetOperator

Create createDemographicSubset Subset operator

createEmptyCohortDefinitionSet

Create an empty cohort definition set

createEmptyNegativeControlOutcomeCohortSet

Create an empty negative control outcome cohort set

createLimitSubset

Create Limit Subset Operator

createLimitSubsetOperator

Create Limit Subset Operator

createResultsDataModel

Create the results data model tables on a database server.

createRxNormCohortTemplateDefinition

Create Rx Norm Cohort Template Definition

createSnomedCohortTemplateDefinition

Create SNOMED Cohort Template Definition

createSubsetCohortWindow

Create a relative time window for cohort subset operations

createUnionCohortTemplate

Create cohort template to union multiple cohorts

DemographicSubsetOperator

Demographic Subset Operator

dropCohortStatsTables

Drop cohort statistics tables

exportCohortStatsTables

Export the cohort statistics tables to the file system

generateCohortSet

Generate a set of cohorts

generateNegativeControlOutcomeCohorts

Generate a set of negative control outcome cohorts

getCohortCounts

Count the cohort(s)

getCohortDefinitionSet

Get a cohort definition set

getCohortInclusionRules

Get Cohort Inclusion Rules from a cohort definition set

getCohortStats

Get Cohort Inclusion Stats Table Data

getCohortTableNames

Used to get a list of cohort table names to use when creating the coho...

getCohortValidationCounts

Validate cohort

getDataMigrator

Get database migrations instance

getExcludeOnIndexSubsetDefinitionIds

Get Exclude On Index Subset Definition Ids

getIndicationSubsetDefinitionIds

Get Indication Subset Definition Ids

getLastGeneratedCohortChecksums

Get last generated cohort checksums

getRestrictionSubsetDefinitionIds

Get Restriction Subset Definition Ids

getResultsDataModelSpecifications

Get specifications for CohortGenerator results data model

getSubsetDefinitions

Get cohort subset definitions from a cohort definition set

getTemplateDefinitions

Extract template definitions from a cohort definition set

insertInclusionRuleNames

Used to insert the inclusion rule names from a cohort definition set w...

isCamelCase

Used to check if a string is in lower camel case

isCohortDefinitionSet

Is the data.frame a cohort definition set?

isFormattedForDatabaseUpload

Is the data.frame formatted for uploading to a database?

isSnakeCase

Used to check if a string is in snake case

LimitSubsetOperator

Limit Subset Operator

migrateDataModel

Migrate Data model

readCsv

Used to read a .csv file

runCohortGeneration

Run a cohort generation and export results

sampleCohortDefinitionSet

Sample Cohort Definition Set

saveCohortDefinitionSet

Save the cohort definition set to the file system

saveCohortSubsetDefinition

Save cohort subset definitions to json

SubsetCohortWindow

Time Window For Cohort Subset Operator

SubsetOperator

Abstract base class for subsets.

uploadResults

Upload results to the database server.

writeCsv

Used to write a .csv file

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>).

  • Maintainer: Anthony Sena
  • License: Apache License
  • Last published: 2026-02-10 17:10:03 UTC