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Generate cohorts with the HADES CohortGenerator Package

Source: R/Module-CohortGenerator.R
CohortGeneratorModule.Rd

Generates cohorts against the OMOP Common Data Model

Super class

Strategus::StrategusModule -> CohortGeneratorModule

Public fields

cohortDefinitionSharedResourcesClassName

A constant for the name of the cohort definition shared resources section of the analysis specification

negativeControlOutcomeSharedResourcesClassName

A constant for the name of the negative control outcome shared resources section of the analysis specification

Methods

Public methods

Inherited methods

Method new()

Initialize the module

Usage

CohortGeneratorModule$new()

Method execute()

Generates the cohorts

Usage

CohortGeneratorModule$execute(
  connectionDetails,
  analysisSpecifications,
  executionSettings
)

Arguments

connectionDetails

An object of class connectionDetails as created by the DatabaseConnector::createConnectionDetails() function.

analysisSpecifications

An object of type AnalysisSpecifications as created by createEmptyAnalysisSpecificiations().

analysisSpecifications

An object of type AnalysisSpecifications as created by createEmptyAnalysisSpecificiations().

executionSettings

An object of type ExecutionSettings as created by createCdmExecutionSettings() or createResultsExecutionSettings().

Method createResultsDataModel()

Create the results data model for the module

Usage

CohortGeneratorModule$createResultsDataModel(
  resultsConnectionDetails,
  resultsDatabaseSchema,
  tablePrefix = ""
)

Arguments

resultsConnectionDetails

The connection details to the results database which is an object of class connectionDetails as created by the DatabaseConnector::createConnectionDetails() function.

resultsConnectionDetails

The connection details to the results database which is an object of class connectionDetails as created by the DatabaseConnector::createConnectionDetails() function.

resultsDatabaseSchema

The schema in the results database that holds the results data model.

tablePrefix

A prefix to apply to the database table names (optional).

tablePrefix

A prefix to apply to the database table names (optional).

Method getResultsDataModelSpecification()

Get the results data model specification for the module

Usage

CohortGeneratorModule$getResultsDataModelSpecification(tablePrefix = "")

Arguments

tablePrefix

A prefix to apply to the database table names (optional).

tablePrefix

A prefix to apply to the database table names (optional).

Method uploadResults()

Upload the results for the module

Usage

CohortGeneratorModule$uploadResults(
  resultsConnectionDetails,
  analysisSpecifications,
  resultsDataModelSettings
)

Arguments

resultsConnectionDetails

The connection details to the results database which is an object of class connectionDetails as created by the DatabaseConnector::createConnectionDetails() function.

resultsConnectionDetails

The connection details to the results database which is an object of class connectionDetails as created by the DatabaseConnector::createConnectionDetails() function.

analysisSpecifications

An object of type AnalysisSpecifications as created by createEmptyAnalysisSpecificiations().

analysisSpecifications

An object of type AnalysisSpecifications as created by createEmptyAnalysisSpecificiations().

resultsDataModelSettings

The results data model settings as created using [@seealso createResultsDataModelSettings()]

Method createModuleSpecifications()

Creates the CohortGenerator Module Specifications

Usage

CohortGeneratorModule$createModuleSpecifications(generateStats = TRUE)

Arguments

generateStats

When TRUE, the Circe cohort definition SQL will include steps to compute inclusion rule statistics.

Method createCohortSharedResourceSpecifications()

Create shared specifications for the cohort definition set

Usage

CohortGeneratorModule$createCohortSharedResourceSpecifications(
  cohortDefinitionSet
)

Arguments

cohortDefinitionSet

The cohort definition set to include in the specification. See the CohortGenerator package for details on how to build this object.

Method createNegativeControlOutcomeCohortSharedResourceSpecifications()

Create shared specifications for the negative control outcomes cohort set

Usage

CohortGeneratorModule$createNegativeControlOutcomeCohortSharedResourceSpecifications(
  negativeControlOutcomeCohortSet,
  occurrenceType,
  detectOnDescendants
)

Arguments

negativeControlOutcomeCohortSet

The negative control outcome cohort definition set defines the concepts to use to construct negative control outcome cohorts. See the CohortGenerator package for more details.

occurrenceType

Either "first" or "all

detectOnDescendants

When TRUE, the concept ID for the negative control will use the concept_ancestor table and will detect descendant concepts when constructing the cohort.

Method validateModuleSpecifications()

Validate the module specifications

Usage

CohortGeneratorModule$validateModuleSpecifications(moduleSpecifications)

Arguments

moduleSpecifications

The CohortGenerator module specifications

Method validateCohortSharedResourceSpecifications()

Validate the cohort shared resource specifications

Usage

CohortGeneratorModule$validateCohortSharedResourceSpecifications(
  cohortSharedResourceSpecifications
)

Arguments

cohortSharedResourceSpecifications

The cohort shared resource specifications

Method validateNegativeControlOutcomeCohortSharedResourceSpecifications()

Validate the cohort shared resource specifications

Usage

CohortGeneratorModule$validateNegativeControlOutcomeCohortSharedResourceSpecifications(
  negativeControlOutcomeCohortSharedResourceSpecifications
)

Arguments

negativeControlOutcomeCohortSharedResourceSpecifications

The cohort shared resource specifications

Method clone()

The objects of this class are cloneable with this method.

Usage

CohortGeneratorModule$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.