requireTableIntersect: Require cohort subjects are present in another clinical table

In CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model

Require cohort subjects are present in another clinical table

Description

requireTableIntersect() filters a cohort table based on a requirement that an individual is seen (or not seen) to have a record (or no records) in a clinical table in some time window around an index date.

Usage

requireTableIntersect(
  cohort,
  tableName,
  window,
  intersections = c(1, Inf),
  cohortId = NULL,
  indexDate = "cohort_start_date",
  targetStartDate = startDateColumn(tableName),
  targetEndDate = endDateColumn(tableName),
  inObservation = TRUE,
  censorDate = NULL,
  name = tableName(cohort),
  .softValidation = TRUE
)

Arguments

cohort	A cohort table in a cdm reference.
tableName	Name of the table to check for intersect.
window	A list of vectors specifying minimum and maximum days from indexDate to consider events over.
intersections	A range indicating number of intersections for criteria to be fulfilled. If a single number is passed, the number of intersections must match this.
cohortId	Vector identifying which cohorts to modify (cohort_definition_id or cohort_name). If NULL, all cohorts will be used; otherwise, only the specified cohorts will be modified, and the rest will remain unchanged.
indexDate	Name of the column in the cohort that contains the date to compute the intersection.
targetStartDate	Start date of reference in cohort table.
targetEndDate	End date of reference in cohort table. If NULL, incidence of target event in the window will be considered as intersection, otherwise prevalence of that event will be used as intersection (overlap between cohort and event).
inObservation	If TRUE only records inside an observation period will be considered.
censorDate	Whether to censor overlap events at a specific date or a column date of the cohort.
name	Name of the new cohort table created in the cdm object.
.softValidation	Whether to perform a soft validation of consistency. If set to FALSE four additional checks will be performed: 1) a check that cohort end date is not before cohort start date, 2) a check that there are no missing values in required columns, 3) a check that cohort duration is all within observation period, and 4) that there are no overlapping cohort entries

Value

Cohort table with only those in the other table kept (or those that are not in the table if negate = TRUE)

Examples

library(CohortConstructor)
cdm <- mockCohortConstructor(drugExposure = TRUE)
cdm$cohort1 |>
  requireTableIntersect(tableName = "drug_exposure",
                            indexDate = "cohort_start_date",
                            window = c(-Inf, 0))

CohortConstructor documentation built on June 8, 2025, 12:49 p.m.