Package index

Create analysis specifications

Functions for creating the analysis specification to execute. An analysis specification includes one or more Strategus HADES module settings which are added to the analysis specification.

addCharacterizationModuleSpecifications(): Add Characterization module specifications to analysis specifications

addCohortDiagnosticsModuleSpecifications(): Add Cohort Diagnostics module specifications to analysis specifications

addCohortGeneratorModuleSpecifications(): Add Cohort Generator module specifications to analysis specifications

addCohortIncidenceModuleSpecifications(): Add Cohort Incidence module specifications to analysis specifications

addCohortMethodeModuleSpecifications(): Add Cohort Method module specifications to analysis specifications

addEvidenceSynthesisModuleSpecifications(): Add Evidence Synthesis module specifications to analysis specifications

addModuleSpecifications(): Add generic module specifications to analysis specifications

addPatientLevelPredictionModuleSpecifications(): Add Patient Level Prediction module specifications to analysis specifications

addSelfControlledCaseSeriesModuleSpecifications(): Add Self Controlled Case Series Module module specifications to analysis specifications

addSharedResources(): Add shared resources (i.e. cohorts) to analysis specifications

createEmptyAnalysisSpecificiations(): Create an empty analysis specifications object.

Executing a study

These functions are used to create the settings necessary to execute a study as defined by the contents of the analysis specification.

execute(): Execute analysis specifications.

createCdmExecutionSettings(): Create CDM execution settings

createResultsExecutionSettings(): Create Results execution settings

getCdmDatabaseMetaData(): Gets the metadata for your OMOP CDM Database

HADES Modules

OMOP CDM HADES Modules

These modules are designed to run against your OMOP CDM to carry out their analyses.

CharacterizationModule: Characterize cohorts with the HADES Characterization Package

CohortDiagnosticsModule: Evaluate phenotypes with the HADES CohortDiagnostics Package

CohortGeneratorModule: Generate cohorts with the HADES CohortGenerator Package

CohortIncidenceModule: Compute incidence with the HADES CohortIncidence Package

CohortMethodModule: New-user cohort studies with the HADES CohortMethod Package

PatientLevelPredictionModule: Patient-level prediction with the HADES PatientLevelPrediction Package

SelfControlledCaseSeriesModule: Self-Controlled Case Series design with the HADES SelfControlledCaseSeries Package

Results HADES Modules

These modules are designed to run against results that are produced by one or more OMOP CDM HADES Modules. Results must be stored in a PostgreSQL database.

EvidenceSynthesisModule: Meta-analysis with the HADES EvidenceSynthesis Package

Results Data Model Creation & Upload

These functions are used to create the PostgreSQL results data model tables and to upload results produced by the HADES modules.

createResultDataModel(): Create Result Data Model

createResultsDataModelSettings(): Create Results Data Model Settings

uploadResults(): Upload results

These functions are used to prepare results to share with a network study coordinator

zipResults(): Create a zip file with all study results for sharing with study coordinator

Internal R6 Class

This is a list of internal classes used by Strategus developers

StrategusModule: StrategusModule defines the base class for each HADES module