Patient-level prediction with the HADES PatientLevelPrediction Package

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

Super class

Strategus::StrategusModule -> PatientLevelPredictionModule

Public fields

tablePrefix

The table prefix to append to the results tables

Methods

Public methods

• PatientLevelPredictionModule$new()

• PatientLevelPredictionModule$execute()

• PatientLevelPredictionModule$createResultsDataModel()

• PatientLevelPredictionModule$getResultsDataModelSpecification()

• PatientLevelPredictionModule$uploadResults()

• PatientLevelPredictionModule$createModuleSpecifications()

• PatientLevelPredictionModule$validateModuleSpecifications()

• PatientLevelPredictionModule$clone()

Inherited methods

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

---

Method new()

Initialize the module

Usage

PatientLevelPredictionModule$new()

---

Method execute()

Executes the PatientLevelPrediction package

Usage

PatientLevelPredictionModule$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().

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Method createResultsDataModel()

Create the results data model for the module

Usage

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

PatientLevelPredictionModule$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

PatientLevelPredictionModule$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 PatientLevelPrediction Module Specifications

Usage

PatientLevelPredictionModule$createModuleSpecifications(
  modelDesignList,
  skipDiagnostics = FALSE
)

Arguments

modelDesignList

A list of model designs created using PatientLevelPrediction::createModelDesign()

skipDiagnostics

Whether to run the diagnostics based on PROBAST before model development

---

Method validateModuleSpecifications()

Validate the module specifications

Usage

PatientLevelPredictionModule$validateModuleSpecifications(moduleSpecifications)

Arguments

moduleSpecifications

The PatientLevelPrediction module specifications

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Method clone()

The objects of this class are cloneable with this method.

Usage

PatientLevelPredictionModule$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.