Run a list of analyses

Run a list of analyses

runSccAnalyses(
  connectionDetails,
  cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  exposureDatabaseSchema = cdmDatabaseSchema,
  exposureTable = "drug_era",
  outcomeDatabaseSchema = cdmDatabaseSchema,
  outcomeTable = "condition_occurrence",
  resultsFolder = "./SelfControlledCohortOutput",
  sccAnalysisList,
  exposureOutcomeList,
  databaseId,
  controlType = "outcome",
  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.

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.

resultsFolder

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.

databaseId

Unique identifier for database - required

controlType

Calibrate effect estimates with outcome (default) or exposure controls

analysisThreads

The number of parallel threads to use to execute the analyses.

computeThreads

Number of parallel threads for computing IRRs with exact confidence intervals.

Value

Invisibly returns a data frame containing a reference table for all exposure-outcome-analysis combinations executed.

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)`.

Examples

if (FALSE) { # \dontrun{
connectionDetails <- Eunomia::getEunomiaConnectionDetails()

eo1 <- createExposureOutcome(exposureId = 1124300, outcomeId = 444382)
analysis1 <- createSccAnalysis(analysisId = 1,
                              description = "Main analysis",
                              runSelfControlledCohortArgs = createRunSelfControlledCohortArgs())

results <- runSccAnalyses(
  connectionDetails = connectionDetails,
  cdmDatabaseSchema = "main",
  exposureOutcomeList = list(eo1),
  sccAnalysisList = list(analysis1),
  databaseId = "Eunomia",
  resultsFolder = "./results"
)
} # }