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{
library(PatientProfiles)
cdm <- mockPatientProfiles(source = "duckdb")
cdm$cohort1 |>
addTableIntersectFlag(tableName = "visit_occurrence")
#> # Source: table<og_143_1757798581> [?? x 5]
#> # Database: DuckDB 1.3.3-dev231 [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 9 1948-07-14 1950-03-26
#> 2 2 10 1965-09-17 1979-05-03
#> 3 3 5 1965-11-01 2004-01-23
#> 4 1 6 2010-08-14 2021-10-08
#> 5 2 2 1959-12-01 1969-06-22
#> 6 3 7 1959-10-19 1963-01-27
#> 7 1 4 1945-02-27 1959-08-25
#> 8 1 8 1982-03-04 2016-07-21
#> 9 2 3 1961-12-15 1961-12-17
#> 10 3 1 1924-10-04 1932-11-24
#> # ℹ 1 more variable: visit_occurrence_0_to_inf <dbl>
# }