getSccRiskWindowStats: Get Self-Controlled Cohort Risk Window Statistics

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

Get Self-Controlled Cohort Risk Window Statistics

Description

Compute statistics from risk windows.

Usage

getSccRiskWindowStats(
  connection,
  outcomeDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  oracleTempSchema = NULL,
  outcomeIds = NULL,
  cdmVersion = 5,
  outcomeTable = "condition_era",
  firstOutcomeOnly = TRUE,
  resultsDatabaseSchema = NULL,
  riskWindowsTable = "#risk_windows"
)

Arguments

connection	DatabaseConnector connection instance
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.
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.
outcomeIds	The condition_concept_ids or cohort_definition_ids of the outcomes of interest. If empty, all the outcomes in the outcome table will be included.
cdmVersion	Define the OMOP CDM version used: currently support "4" and "5".
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.
firstOutcomeOnly	If TRUE, only use first occurrence of each condition concept id for each person.
resultsDatabaseSchema	Schema to oputput results to. Ignored if resultsTable and riskWindowsTable are temporary.
riskWindowsTable	String: optionally store the risk windows in a (non-temporary) table.

Details

Requires a risk window table to be created first with 'runSccRiskWindows'

Value

list containing data frames: treatmentTimeDistribution, timeToOutcomeDistribution, timeToOutcomeDistributionExposed, timeToOutcomeDistributionUnexposed

Examples

## Not run: 
# First, create the risk windows table
connectionDetails <- Eunomia::getEunomiaConnectionDetails()
connection <- DatabaseConnector::connect(connectionDetails)
riskWindowsTable <- "computed_risk_windows"
runSccRiskWindows(connection,
                  cdmDatabaseSchema = "main",
                  exposureIds = c(1102527, 1125315),
                  resultsDatabaseSchema = "main", # This is the schema where the results will be stored
                  riskWindowsTable = riskWindowsTable,
                  exposureTable = "drug_era")
# Get stats based on outcomes of interest
tarStats <- getSccRiskWindowStats(connection,
                                  outcomeDatabaseSchema = "main",
                                  resultsDatabaseSchema = "main",
                                  riskWindowsTable = riskWindowsTable,
                                  outcomeTable = "condition_era",
                                  outcomeIds = 192671)

## End(Not run)

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