Compute a flag intersect with an omop table.
Usage
addTableIntersectFlag(
x,
tableName,
indexDate = "cohort_start_date",
censorDate = NULL,
window = list(c(0, Inf)),
targetStartDate = startDateColumn(tableName),
targetEndDate = endDateColumn(tableName),
inObservation = TRUE,
nameStyle = "{table_name}_{window_name}",
name = NULL
)Arguments
- x
Table with individuals in the cdm.
- tableName
Name of the table to intersect with. Options: visit_occurrence, condition_occurrence, drug_exposure, procedure_occurrence, device_exposure, measurement, observation, drug_era, condition_era, specimen, episode.
- 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.
- window
window to consider events in.
- targetStartDate
Column name with start date for comparison.
- targetEndDate
Column name with end date for comparison.
- inObservation
If TRUE only records inside an observation period will be considered.
- nameStyle
naming of the added column or columns, should include required parameters.
- name
Name of the new table, if NULL a temporary table is returned.
Examples
# \donttest{
cdm <- mockPatientProfiles()
cdm$cohort1 |>
addTableIntersectFlag(tableName = "visit_occurrence")
#> # Source: table<og_149_1740755743> [?? x 5]
#> # Database: DuckDB v1.2.0 [unknown@Linux 6.8.0-1021-azure:R 4.4.2/:memory:]
#> cohort_definition_id subject_id cohort_start_date cohort_end_date
#> <int> <int> <date> <date>
#> 1 1 2 1962-04-25 1965-03-11
#> 2 2 10 1961-11-25 1962-12-19
#> 3 2 3 1918-09-16 1922-05-04
#> 4 2 5 1920-08-07 1927-01-02
#> 5 3 1 1947-09-12 1948-08-15
#> 6 2 8 1933-01-06 1934-05-20
#> 7 1 6 1928-02-29 1928-03-07
#> 8 1 9 1978-03-11 1998-09-07
#> 9 1 4 2014-01-22 2014-05-25
#> 10 1 7 1981-11-27 1981-12-14
#> # ℹ 1 more variable: visit_occurrence_0_to_inf <dbl>
mockDisconnect(cdm = cdm)
# }