Characterize cohorts with the HADES Characterization Package

Computes cohort characterization information against the OMOP Common Data Model

Super class

StrategusModule -> CharacterizationModule

Public fields

tablePrefix: The table prefix to append to the results tables

Methods

Public methods

CharacterizationModule$new()
CharacterizationModule$execute()
CharacterizationModule$createResultsDataModel()
CharacterizationModule$getResultsDataModelSpecification()
CharacterizationModule$uploadResults()
CharacterizationModule$createModuleSpecifications()
CharacterizationModule$clone()

Inherited methods

`CharacterizationModule$new()`

Initialize the module

Usage

CharacterizationModule$new()

`CharacterizationModule$execute()`

Execute characterization

Usage

CharacterizationModule$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().

`CharacterizationModule$createResultsDataModel()`

Create the results data model for the module

Usage

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

`CharacterizationModule$getResultsDataModelSpecification()`

Get the results data model specification for the module

Usage

CharacterizationModule$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).

`CharacterizationModule$uploadResults()`

Upload the results for the module

Usage

CharacterizationModule$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().

`CharacterizationModule$createModuleSpecifications()`

Creates the CharacterizationModule Specifications

Usage

CharacterizationModule$createModuleSpecifications(
  characterizationSettings = NULL,
  targetIds = NULL,
  limitToFirstInNDays = NULL,
  minPriorObservation = NULL,
  outcomeIds = NULL,
  outcomeWashoutDays = NULL,
  riskWindowStart = NULL,
  startAnchor = NULL,
  riskWindowEnd = NULL,
  endAnchor = NULL,
  dechallengeStopInterval = NULL,
  dechallengeEvaluationWindow = NULL,
  covariateSettings = NULL,
  caseCovariateSettings = NULL,
  casePreTargetDuration = NULL,
  casePostOutcomeDuration = NULL,
  includeTimeToEvent = NULL,
  includeDechallengeRechallenge = NULL,
  includeTargetBaseline = NULL,
  includeRiskFactors = NULL,
  includeCaseSeries = NULL,
  mode = "CohortIncidence",
  minSMD = 0,
  minCharacterizationMean = 0,
  minCovariateCount = 0,
  minTargetSize = 0,
  minCaseSize = 0,
  outputTable = "characterization_cohorts"
)

Arguments

characterizationSettings: The settings defined using Characterization::createCharacterizationSettings
targetIds: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
limitToFirstInNDays: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
minPriorObservation: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
outcomeIds: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
outcomeWashoutDays: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
riskWindowStart: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
startAnchor: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
riskWindowEnd: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
endAnchor: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
dechallengeStopInterval: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
dechallengeEvaluationWindow: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
covariateSettings: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
caseCovariateSettings: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
casePreTargetDuration: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
casePostOutcomeDuration: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
includeTimeToEvent: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
includeDechallengeRechallenge: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
includeTargetBaseline: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
includeRiskFactors: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
includeCaseSeries: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
mode: Pick one of 'CohortIncidence'/'Efficient'/'PatientLevelPrediction' to specify how the non-cases are defined
minSMD: The minimum standardized mean difference for the risk factors analysis
minCharacterizationMean: The minimum fraction patients in the target have a covariate for it to be included
minCovariateCount: The minimum number of patients in the analysis to have a covariate for it to be included
minTargetSize: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
minCaseSize: Deprecated. Use Characterization v4 settings objects via characterizationSettings.
outputTable: The table used by characterization to create the cohorts used in characterization (included targets, cases, non-cases, etc.). The spec hash and database hash are added to this name to make it unique per run.

`CharacterizationModule$clone()`

The objects of this class are cloneable with this method.

Usage

CharacterizationModule$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.