Require cohort subjects are present in another clinical table

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,
  atFirst = FALSE,
  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.

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.

.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

Examples

# \donttest{
library(CohortConstructor)
cdm <- mockCohortConstructor(drugExposure = TRUE)
cdm$cohort1 |>
  requireTableIntersect(tableName = "drug_exposure",
                            indexDate = "cohort_start_date",
                            window = c(-Inf, 0))
#> # Source:   table<cohort1> [?? x 4]
#> # Database: DuckDB v1.3.2 [unknown@Linux 6.11.0-1018-azure:R 4.5.1/:memory:]
#>    cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                   <int>      <int> <date>            <date>         
#>  1                    1          2 2010-03-30        2010-04-20     
#>  2                    1          3 2005-09-25        2007-04-24     
#>  3                    1          3 2007-04-25        2007-07-09     
#>  4                    1          3 2007-07-10        2007-11-24     
#>  5                    1          4 2017-05-07        2017-07-06     
#>  6                    1          5 2016-08-28        2016-10-13     
#>  7                    1          5 2016-11-01        2016-12-06     
#>  8                    1          6 1994-11-23        2001-04-26     
#>  9                    1          6 2014-10-27        2014-12-11     
#> 10                    1          9 2007-03-19        2007-09-15     
# }