Compute the intersect with a target cohort, you can compute the number of occurrences, a flag of presence, a certain date and/or the time difference

Usage

addCohortIntersect(
  x,
  cdm = lifecycle::deprecated(),
  targetCohortTable,
  targetCohortId = NULL,
  indexDate = "cohort_start_date",
  censorDate = NULL,
  targetStartDate = "cohort_start_date",
  targetEndDate = "cohort_end_date",
  window = list(c(0, Inf)),
  order = "first",
  flag = TRUE,
  count = TRUE,
  date = TRUE,
  days = TRUE,
  nameStyle = "{value}_{cohort_name}_{window_name}"
)

Arguments

x: Table with individuals in the cdm.
cdm: Object that contains a cdm reference. Use CDMConnector to obtain a cdm reference.
targetCohortTable: name of the cohort that we want to check for overlap.
targetCohortId: vector of cohort definition ids to include.
indexDate: Variable in x that contains the date to compute the intersection.
censorDate: whether to censor overlap events at a specific date or a column date of x.
targetStartDate: date of reference in cohort table, either for start (in overlap) or on its own (for incidence).
targetEndDate: date of reference in cohort table, either for end (overlap) or NULL (if incidence).
window: window to consider events of.
order: which record is considered in case of multiple records.
flag: TRUE or FALSE. If TRUE, flag will calculated for this intersection.
count: TRUE or FALSE. If TRUE, the number of counts will be calculated for this intersection.
date: TRUE or FALSE. If TRUE, date will be calculated for this intersection.
days: TRUE or FALSE. If TRUE, time difference in days will be calculated for this intersection.
nameStyle: naming of the added column or columns, should include required parameters.

Value

table with added columns with overlap information.

Examples

# \donttest{
cdm <- mockPatientProfiles()

cdm$cohort1 %>%
  addCohortIntersect(
    targetCohortTable = "cohort2"
  )
#> Warning: `addCohortIntersect()` was deprecated in PatientProfiles 0.6.0.
#> please use the specific functions instead:
#> • addCohortIntersectFlag()
#> • addCohortIntersectCount()
#> • addCohortIntersectDate()
#> • addCohortIntersectDays()
#> # Source:   table<og_014_1714466018> [2 x 12]
#> # Database: DuckDB v0.10.1 [unknown@Linux 6.5.0-1018-azure:R 4.4.0/:memory:]
#>   cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                  <dbl>      <dbl> <date>            <date>         
#> 1                    1          1 2020-01-01        2020-04-01     
#> 2                    1          1 2020-06-01        2020-08-01     
#> # ℹ 8 more variables: count_cohort_1_0_to_inf <dbl>,
#> #   count_cohort_2_0_to_inf <dbl>, flag_cohort_1_0_to_inf <dbl>,
#> #   flag_cohort_2_0_to_inf <dbl>, date_cohort_2_0_to_inf <date>,
#> #   date_cohort_1_0_to_inf <date>, days_cohort_2_0_to_inf <dbl>,
#> #   days_cohort_1_0_to_inf <dbl>
CDMConnector::cdmDisconnect(cdm = cdm)
# }