Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect • CohortConstructor

requireConceptIntersect() filters a cohort table based on a requirement that an individual is seen (or not seen) to have events related to a concept list in some time window around an index date.

Usage

requireConceptIntersect(
  cohort,
  conceptSet,
  window,
  intersections = c(1, Inf),
  cohortId = NULL,
  indexDate = "cohort_start_date",
  targetStartDate = "event_start_date",
  targetEndDate = "event_end_date",
  inObservation = TRUE,
  censorDate = NULL,
  name = tableName(cohort)
)

Arguments

cohort: A cohort table in a cdm reference.
conceptSet: A conceptSet, which can either be a codelist or a conceptSetExpression.
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.

Value

Cohort table with only those with the events in the concept list kept (or those without the event if negate = TRUE)

Examples

# \donttest{
library(CohortConstructor)
cdm <- mockCohortConstructor(conditionOccurrence = TRUE)
cdm$cohort2 <-  requireConceptIntersect(
  cohort = cdm$cohort1,
  conceptSet = list(a = 194152),
  window = c(-Inf, 0),
  name = "cohort2")
#> Warning: ! `codelist` contains numeric values, they are casted to integers.
  # }