Run a list of analyses — runSccAnalyses • SelfControlledCohort

Run a list of analyses

runSccAnalyses(
  connectionDetails,
  cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  oracleTempSchema = NULL,
  exposureDatabaseSchema = cdmDatabaseSchema,
  exposureTable = "drug_era",
  outcomeDatabaseSchema = cdmDatabaseSchema,
  outcomeTable = "condition_occurrence",
  cdmVersion = 5,
  outputFolder = "./SelfControlledCohortOutput",
  sccAnalysisList,
  exposureOutcomeList,
  analysisThreads = 1,
  computeThreads = 1
)

Arguments

connectionDetails: An R object of type connectionDetails created using the function createConnectionDetails in the DatabaseConnector package.
cdmDatabaseSchema: Name of database schema that contains the OMOP CDM and vocabulary.
tempEmulationSchema: Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
oracleTempSchema: For Oracle only: the name of the database schema where you want all temporary tables to be managed. Requires create/insert permissions to this database.
exposureDatabaseSchema: The name of the database schema that is the location where the exposure data used to define the exposure cohorts is available. If exposureTable = DRUG_ERA, exposureDatabaseSchema is not used by assumed to be cdmSchema. Requires read permissions to this database.
exposureTable: The tablename that contains the exposure cohorts. If exposureTable <> DRUG_ERA, then expectation is exposureTable has format of COHORT table: cohort_concept_id, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
outcomeDatabaseSchema: The name of the database schema that is the location where the data used to define the outcome cohorts is available. If exposureTable = CONDITION_ERA, exposureDatabaseSchema is not used by assumed to be cdmSchema. Requires read permissions to this database.
outcomeTable: The tablename that contains the outcome cohorts. If outcomeTable <> CONDITION_OCCURRENCE, then expectation is outcomeTable has format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
cdmVersion: Define the OMOP CDM version used: currently support "4" and "5".
outputFolder: Name of the folder where all the outputs will written to.
sccAnalysisList: A list of objects of type sccAnalysis as created using the createSccAnalysis function.
exposureOutcomeList: A list of objects of type exposureOutcome as created using the createExposureOutcome function.
analysisThreads: The number of parallel threads to use to execute the analyses.
computeThreads: Number of parallel threads for computing IRRs with exact confidence intervals.

Details

Run a list of analyses for the drug-comparator-outcomes of interest. This function will run all specified analyses against all hypotheses of interest, meaning that the total number of outcome models is `length(cmAnalysisList) * length(drugComparatorOutcomesList)`.