Self-Controlled Case Series design with the HADES SelfControlledCaseSeries Package

Module for performing Self-Controlled Case Series (SCCS) analyses against the OMOP Common Data Model.

Super class

Strategus::StrategusModule -> SelfControlledCaseSeriesModule

Public fields

tablePrefix

The table prefix for results tables

Methods

Public methods

• SelfControlledCaseSeriesModule$new()

• SelfControlledCaseSeriesModule$execute()

• SelfControlledCaseSeriesModule$createResultsDataModel()

• SelfControlledCaseSeriesModule$getResultsDataModelSpecification()

• SelfControlledCaseSeriesModule$uploadResults()

• SelfControlledCaseSeriesModule$createModuleSpecifications()

• SelfControlledCaseSeriesModule$validateModuleSpecifications()

• SelfControlledCaseSeriesModule$clone()

Inherited methods

• Strategus::StrategusModule$createSharedResourcesSpecifications()
• Strategus::StrategusModule$validateSharedResourcesSpecifications()

---

Method new()

Initialize the module

Usage

SelfControlledCaseSeriesModule$new()

---

Method execute()

Executes the SelfControlledCaseSeries package

Usage

SelfControlledCaseSeriesModule$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

SelfControlledCaseSeriesModule$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

SelfControlledCaseSeriesModule$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

SelfControlledCaseSeriesModule$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 SelfControlledCaseSeries Module Specifications

Usage

SelfControlledCaseSeriesModule$createModuleSpecifications(
  sccsAnalysesSpecifications,
  sccsAnalysisList = NULL,
  exposuresOutcomeList = NULL,
  analysesToExclude = NULL,
  combineDataFetchAcrossOutcomes = NULL,
  sccsDiagnosticThresholds = NULL
)

Arguments

sccsAnalysesSpecifications

An R6 class created by SelfControlledCaseSeries::createSccsAnalysesSpecifications

sccsAnalysisList

Deprecated with SelfControlledCaseSeries v6 - please use the sccsAnalysesSpecifications parameter instead.

exposuresOutcomeList

Deprecated with SelfControlledCaseSeries v6 - please use the sccsAnalysesSpecifications parameter instead.

analysesToExclude

Deprecated with SelfControlledCaseSeries v6 - please use the sccsAnalysesSpecifications parameter instead.

combineDataFetchAcrossOutcomes

Deprecated with SelfControlledCaseSeries v6 - please use the sccsAnalysesSpecifications parameter instead.

sccsDiagnosticThresholds

Deprecated with SelfControlledCaseSeries v6 - please use the sccsAnalysesSpecifications parameter instead.

---

Method validateModuleSpecifications()

Validate the module specifications

Usage

SelfControlledCaseSeriesModule$validateModuleSpecifications(
  moduleSpecifications
)

Arguments

moduleSpecifications

The SelfControlledCaseSeries module specifications

---

Method clone()

The objects of this class are cloneable with this method.

Usage

SelfControlledCaseSeriesModule$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.