runSccRiskWindows: Run Self-Controlled Cohort Risk Windows

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

Run Self-Controlled Cohort Risk Windows

Description

Compute time at risk exposed and time at risk unexposed for risk window parameters. See 'getSccRiskWindowStats' for example usage.

Usage

runSccRiskWindows(
  connection,
  cdmDatabaseSchema,
  cdmVersion = 5,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  oracleTempSchema = NULL,
  exposureIds = NULL,
  exposureDatabaseSchema = cdmDatabaseSchema,
  exposureTable = "drug_era",
  firstExposureOnly = TRUE,
  minAge = "",
  maxAge = "",
  studyStartDate = "",
  studyEndDate = "",
  addLengthOfExposureExposed = TRUE,
  riskWindowStartExposed = 1,
  riskWindowEndExposed = 30,
  addLengthOfExposureUnexposed = TRUE,
  riskWindowEndUnexposed = -1,
  riskWindowStartUnexposed = -30,
  hasFullTimeAtRisk = FALSE,
  washoutPeriod = 0,
  followupPeriod = 0,
  riskWindowsTable = "#risk_windows",
  resultsDatabaseSchema = NULL
)

Arguments

connection	DatabaseConnector connection instance
cdmDatabaseSchema	Name of database schema that contains the OMOP CDM and vocabulary.
cdmVersion	Define the OMOP CDM version used: currently support "4" and "5".
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.
exposureIds	A vector containing the drug_concept_ids or cohort_definition_ids of the exposures of interest. If empty, all exposures in the exposure table will be included.
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.
firstExposureOnly	If TRUE, only use first occurrence of each drug concept id for each person
minAge	Integer for minimum allowable age.
maxAge	Integer for maximum allowable age.
studyStartDate	Date for minimum allowable data for index exposure. Date format is 'yyyymmdd'.
studyEndDate	Date for maximum allowable data for index exposure. Date format is 'yyyymmdd'.
addLengthOfExposureExposed	If TRUE, use the duration from drugEraStart -> drugEraEnd as part of timeAtRisk.
riskWindowStartExposed	Integer of days to add to drugEraStart for start of timeAtRisk (0 to include index date, 1 to start the day after).
riskWindowEndExposed	Additional window to add to end of exposure period (if addLengthOfExposureExposed = TRUE, then add to exposure end date, else add to exposure start date).
addLengthOfExposureUnexposed	If TRUE, use the duration from exposure start -> exposure end as part of timeAtRisk looking back before exposure start.
riskWindowEndUnexposed	Integer of days to add to exposure start for end of timeAtRisk (0 to include index date, -1 to end the day before).
riskWindowStartUnexposed	Additional window to add to start of exposure period (if addLengthOfExposureUnexposed = TRUE, then add to exposure end date, else add to exposure start date).
hasFullTimeAtRisk	If TRUE, restrict to people who have full time-at-risk exposed and unexposed.
washoutPeriod	Integer to define required time observed before exposure start.
followupPeriod	Integer to define required time observed after exposure start.
riskWindowsTable	String: optionally store the risk windows in a (non-temporary) table.
resultsDatabaseSchema	Schema to oputput results to. Ignored if resultsTable and riskWindowsTable are temporary.

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