# Cohort Generation for the OMOP Common Data Model

## Documentation for package ‘CohortGenerator’ version 1.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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
CohortSubsetDefinition | Cohort Subset Definition
CohortSubsetOperator | Cohort Subset Operator
CohortTemplateDefinition | Class for automating the creation of bulk cohorts
computeChecksum | Computes the checksum for a value
computeCohortAttrition | Compute cohort attrition from inclusion rule statistics
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
exportCohortSubsetStatsTables | Export cohort subset 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 cohort tables
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 when generating cohorts that include cohort statistics
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
omopCdmDrugExposure | OMOP CDM Drug Exposure Sample Data
omopCdmPerson | OMOP CDM Person Sample Data
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