Skip to contents

Require cohort subjects to have (or not have) events of a concept list

Source: R/requireConceptIntersect.R
requireConceptIntersect.Rd

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,
  cohortCombinationCriteria = "all",
  indexDate = "cohort_start_date",
  targetStartDate = "event_start_date",
  targetEndDate = "event_end_date",
  inObservation = TRUE,
  censorDate = NULL,
  atFirst = FALSE,
  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.

cohortCombinationCriteria

Can be 'all', 'any', or a numeric vector (length 1 or 2) that specifies how many of the target cohorts must meet the intersection requirement. Examples:

  • 'all': must meet criteria for each of the target cohorts.

  • 'any': must meet criteria for only one of the target cohorts.

  • Single value: e.g., 4, exactly 4 cohorts must meet the criteria. If there were 4 target cohorts, this would be the same as 'all'.

  • Range: e.g., c(2, Inf), must meet criteria at last 2 of the target cohorts. Note, c(1, Inf) is equivalent to 'any'.

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.

atFirst

If FALSE the requirement will be applied to all records, if TRUE, it will only be required for the first entry of each subject.

name

Name of the new cohort table created in the cdm object.

Value

Cohort table

Examples

# \donttest{
library(CohortConstructor)
cdm <- mockCohortConstructor()
#> Warning: '/tmp/Rtmpy2Fm44/id_boq' already exists
#> ℹ Reading GiBleed tables.

cdm$cohort2 <-  requireConceptIntersect(
  cohort = cdm$cohort1,
  conceptSet = list(a = 194152),
  window = c(-Inf, 0),
  name = "cohort2")
#> Warning: ! `codelist` casted to integers.
#> ! 1 concept(s) from domain NA eliminated as it is not supported.
#> ℹ Supported domains are: device, specimen, measurement, drug, condition,
#>   observation, procedure, episode, and visit.
# }