Validation of patient-level prediction models with the HADES PatientLevelPrediction Package — PatientLevelPredictionValidationModule • Strategus

Module for performing patient-level prediction model validation for models built using the PatientLevelPrediction package.

Super class

StrategusModule -> PatientLevelPredictionValidationModule

Public fields

tablePrefix: The table prefix to append to the results tables

Methods

Public methods

PatientLevelPredictionValidationModule$new()
PatientLevelPredictionValidationModule$execute()
PatientLevelPredictionValidationModule$createResultsDataModel()
PatientLevelPredictionValidationModule$uploadResults()
PatientLevelPredictionValidationModule$createModuleSpecifications()
PatientLevelPredictionValidationModule$validateModuleSpecifications()
PatientLevelPredictionValidationModule$clone()

Inherited methods

`PatientLevelPredictionValidationModule$new()`

Initialize the module

Usage

PatientLevelPredictionValidationModule$new()

`PatientLevelPredictionValidationModule$execute()`

Executes the PatientLevelPrediction package to validate a PLP model

Usage

PatientLevelPredictionValidationModule$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().

`PatientLevelPredictionValidationModule$createResultsDataModel()`

Create the results data model for the module

Usage

PatientLevelPredictionValidationModule$createResultsDataModel(
  resultsConnectionDetails,
  resultsDatabaseSchema,
  tablePrefix = self$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).

`PatientLevelPredictionValidationModule$uploadResults()`

Upload the results for the module

Usage

PatientLevelPredictionValidationModule$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 createResultsDataModelSettings().

`PatientLevelPredictionValidationModule$createModuleSpecifications()`

Creates the PatientLevelPredictionValidation Module Specifications

Usage

PatientLevelPredictionValidationModule$createModuleSpecifications(
  validationList = list(PatientLevelPrediction::createValidationDesign(plpModelList =
    list(file.path("location_to_model")), targetId = 1, outcomeId = 3,
    restrictPlpDataSettings = PatientLevelPrediction::createRestrictPlpDataSettings(),
    populationSettings = NULL, recalibrate = "weakRecalibration", runCovariateSummary =
    TRUE), PatientLevelPrediction::createValidationDesign(plpModelList =
    list(file.path("location_to_model")), targetId = 4, outcomeId = 3,
    restrictPlpDataSettings = PatientLevelPrediction::createRestrictPlpDataSettings(),

       populationSettings = NULL, recalibrate = "weakRecalibration", runCovariateSummary
    = TRUE)),
  logLevel = "INFO"
)

Arguments

validationList: A list of validation designs from PatientLevelPrediction::createValidationDesign
logLevel: The logging level while executing the model validation.

`PatientLevelPredictionValidationModule$validateModuleSpecifications()`

Validate the module specifications

Usage

PatientLevelPredictionValidationModule$validateModuleSpecifications(
  moduleSpecifications
)

Arguments

moduleSpecifications: The PatientLevelPredictionValidation module specifications

`PatientLevelPredictionValidationModule$clone()`

The objects of this class are cloneable with this method.

Usage

PatientLevelPredictionValidationModule$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.