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Evaluate phenotypes with the HADES CohortDiagnostics Package

Source: R/Module-CohortDiagnostics.R
CohortDiagnosticsModule.Rd

Development and evaluation of phenotype algorithms against the OMOP Common Data Model.

Super class

Strategus::StrategusModule -> CohortDiagnosticsModule

Public fields

tablePrefix

The table prefix to append to results tables

Methods

Public methods

Inherited methods

Method new()

Initialize the module

Usage

CohortDiagnosticsModule$new()

Method execute()

Executes the CohortDiagnostics package

Usage

CohortDiagnosticsModule$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

CohortDiagnosticsModule$createResultsDataModel(
  resultsConnectionDetails,
  resultsDatabaseSchema,
  tablePrefix = self$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

CohortDiagnosticsModule$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

CohortDiagnosticsModule$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 CohortDiagnostics Module Specifications

Usage

CohortDiagnosticsModule$createModuleSpecifications(
  cohortIds = NULL,
  runInclusionStatistics = TRUE,
  runIncludedSourceConcepts = TRUE,
  runOrphanConcepts = TRUE,
  runTimeSeries = FALSE,
  runVisitContext = TRUE,
  runBreakdownIndexEvents = TRUE,
  runIncidenceRate = TRUE,
  runCohortRelationship = TRUE,
  runTemporalCohortCharacterization = TRUE,
  temporalCovariateSettings = private$.getDefaultCovariateSettings(),
  minCharacterizationMean = 0.01,
  irWashoutPeriod = 0
)

Arguments

cohortIds

A list of cohort IDs to use when running the CohortDiagnostics. Default is NULL which will use all cohorts present in the cohort definition set in the analysis specification

runInclusionStatistics

Generate and export statistic on the cohort inclusion rules?

runIncludedSourceConcepts

Generate and export the source concepts included in the cohorts?

runOrphanConcepts

Generate and export potential orphan concepts?

runTimeSeries

Generate and export the time series diagnostics?

runVisitContext

Generate and export index-date visit context?

runBreakdownIndexEvents

Generate and export the breakdown of index events?

runIncidenceRate

Generate and export the cohort incidence rates?

runCohortRelationship

Generate and export the cohort relationship? Cohort relationship checks the temporal relationship between two or more cohorts.

runTemporalCohortCharacterization

Generate and export the temporal cohort characterization? Only records with values greater than 0.001 are returned.

temporalCovariateSettings

Either an object of type covariateSettings as created using one of the createTemporalCovariateSettings function in the FeatureExtraction package, or a list of such objects.

minCharacterizationMean

The minimum mean value for characterization output. Values below this will be cut off from output. This will help reduce the file size of the characterization output, but will remove information on covariates that have very low values. The default is 0.001 (i.e. 0.1 percent)

irWashoutPeriod

Number of days washout to include in calculation of incidence rates - default is 0

Method validateModuleSpecifications()

Validate the module specifications

Usage

CohortDiagnosticsModule$validateModuleSpecifications(moduleSpecifications)

Arguments

moduleSpecifications

The CohortIncidence module specifications

Method clone()

The objects of this class are cloneable with this method.

Usage

CohortDiagnosticsModule$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.