Patient-level prediction with the HADES PatientLevelPrediction Package — PatientLevelPredictionModule • Strategus

Module for performing patient-level prediction in an observational database in the OMOP Common Data Model.

Super class

StrategusModule -> PatientLevelPredictionModule

Inherited methods

Initialize the module

PatientLevelPredictionModule$new()

Executes the PatientLevelPrediction package

PatientLevelPredictionModule$execute(
  connectionDetails,
  analysisSpecifications,
  executionSettings
)

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().

Create the results data model for the module

PatientLevelPredictionModule$createResultsDataModel(
  resultsConnectionDetails,
  resultsDatabaseSchema,
  tablePrefix = self$tablePrefix
)

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).

Get the results data model specification for the module

PatientLevelPredictionModule$getResultsDataModelSpecification(tablePrefix = "")

Upload the results for the module

PatientLevelPredictionModule$uploadResults(
  resultsConnectionDetails,
  analysisSpecifications,
  resultsDataModelSettings
)

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 createResultsDataModelSettings().

Creates the PatientLevelPrediction Module Specifications

PatientLevelPredictionModule$createModuleSpecifications(
  modelDesignList,
  skipDiagnostics = FALSE
)

modelDesignList: A list of model designs created using PatientLevelPrediction::createModelDesign()
skipDiagnostics: Whether to run the diagnostics based on PROBAST before model development

Validate the module specifications

PatientLevelPredictionModule$validateModuleSpecifications(moduleSpecifications)

The objects of this class are cloneable with this method.

PatientLevelPredictionModule$clone(deep = FALSE)