Evaluate phenotype algorithms with the HADES PheValuator Package

Evaluates phenotype algorithms using the PheValuator method against the OMOP Common Data Model.

Super class

StrategusModule -> PheValuatorModule

Public fields

tablePrefix: The table prefix to append to the results tables

Methods

Public methods

PheValuatorModule$new()
PheValuatorModule$execute()
PheValuatorModule$createResultsDataModel()
PheValuatorModule$getResultsDataModelSpecification()
PheValuatorModule$uploadResults()
PheValuatorModule$createModuleSpecifications()
PheValuatorModule$validateModuleSpecifications()
PheValuatorModule$clone()

Inherited methods

`PheValuatorModule$new()`

Initialize the module

Usage

PheValuatorModule$new()

`PheValuatorModule$execute()`

Execute PheValuator

Usage

PheValuatorModule$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().

`PheValuatorModule$createResultsDataModel()`

Create the results data model for the module

Usage

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

`PheValuatorModule$getResultsDataModelSpecification()`

Get the results data model specification for the module

Usage

PheValuatorModule$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).

`PheValuatorModule$uploadResults()`

Upload the results for PheValuator

Usage

PheValuatorModule$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().

`PheValuatorModule$createModuleSpecifications()`

Creates the PheValuator Module Specifications

Usage

PheValuatorModule$createModuleSpecifications(
  analysisName = "Main",
  pheValuatorAnalysisList
)

Arguments

analysisName

A short name for the analysis (default: "Main").

pheValuatorAnalysisList

A list of analysis specification objects. Each element is a list with two named fields:

phenotype

A short file-system-safe name for the phenotype (e.g. "bladderCancer").

cohortsToEvaluate

A list of evaluation parameters:

phenotypeCohortId: Cohort ID(s) of the phenotype to evaluate.
washoutPeriod: Minimum prior observation days (should match cohort definition).
xSpecCohortId: Cohort ID for the extremely-specific (xSpec) cohort.
daysFromxSpec: Days from xSpec cohort start to index visit.
xSensCohortId: Cohort ID for the extremely-sensitive (xSens) cohort.
prevalenceCohortId: Cohort ID used to estimate prevalence.
excludedCovariateConceptIds: Integer vector of concept IDs to exclude from covariates.
covariateSettingsType: One of "chronic" or "acute" (default "chronic").

`PheValuatorModule$validateModuleSpecifications()`

Validate the module specifications

Usage

PheValuatorModule$validateModuleSpecifications(moduleSpecifications)

Arguments

moduleSpecifications: The PheValuator module specifications

`PheValuatorModule$clone()`

The objects of this class are cloneable with this method.

Usage

PheValuatorModule$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.