Run a list of analyses

Usage

runCmAnalyses(
  connectionDetails,
  cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  exposureDatabaseSchema = cdmDatabaseSchema,
  exposureTable = "drug_era",
  outcomeDatabaseSchema = cdmDatabaseSchema,
  outcomeTable = "condition_occurrence",
  nestingCohortDatabaseSchema = cdmDatabaseSchema,
  nestingCohortTable = "cohort",
  outputFolder = "./CohortMethodOutput",
  multiThreadingSettings = createMultiThreadingSettings(),
  cmAnalysesSpecifications
)

Arguments

connectionDetails: An R object of type connectionDetails created using the DatabaseConnector::createConnectionDetails() function.
cdmDatabaseSchema: The name of the database schema that contains the OMOP CDM instance. Requires read permissions to this database. On SQL Server, this should specify both the database and the schema, so for example 'cdm_instance.dbo'.
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_DEFINITION_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.
nestingCohortDatabaseSchema: The name of the database schema that is the location where the data used to define the nesting cohorts is available.
nestingCohortTable: The tablename that contains the nesting cohorts. Must have the format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
outputFolder: Name of the folder where all the outputs will written to.
multiThreadingSettings: An object of type CmMultiThreadingSettings as created using the createMultiThreadingSettings() or createDefaultMultiThreadingSettings() functions.
cmAnalysesSpecifications: An object of type CmAnalysesSpecifications as created using the createCmAnalysesSpecifications().

Value

A tibble describing for each target-comparator-outcome-analysisId combination where the intermediary and outcome model files can be found, relative to the outputFolder.

Details

Run a list of analyses for the target-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(targetComparatorOutcomesList) (if all analyses specify an outcome model should be fitted). When you provide several analyses it will determine whether any of the analyses have anything in common, and will take advantage of this fact. For example, if we specify several analyses that only differ in the way the outcome model is fitted, then this function will extract the data and fit the propensity model only once, and re-use this in all the analysis.

After completion, a tibble containing references to all generated files can be obtained using the getFileReference() function. A summary of the analysis results can be obtained using the getResultsSummary() function. Diagnostics can be loaded using the getDiagnosticsSummary() function.