runSccAnalyses: Run a list of analyses

In OHDSI/SelfControlledCohort: Population-Level Estimation Method that Estimates Incidence Rate Comparison of Exposed/Unexposed Time Within an Exposed Cohort

Run a list of analyses

Description

Run a list of analyses

Usage

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)'.

OHDSI/SelfControlledCohort documentation built on Feb. 22, 2023, 5:44 p.m.