Cohort Generation for the OMOP Common Data Model

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Documentation for package ‘CohortGenerator’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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
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 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