Compute the intersect with an omop table, you can compute the number of occurrences, a flag of presence, a certain date, the time difference and/or obtain a certain column.

Usage

addTableIntersect(
  x,
  tableName,
  indexDate = "cohort_start_date",
  censorDate = NULL,
  window = list(c(0, Inf)),
  order = "first",
  targetStartDate = startDateColumn(tableName),
  targetEndDate = endDateColumn(tableName),
  flag = TRUE,
  count = TRUE,
  date = TRUE,
  days = TRUE,
  field = character(),
  nameStyle = "{table_name}_{value}_{window_name}"
)

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.
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.
order: which record is considered in case of multiple records (only required for date and days options).
targetStartDate: Column name with start date for comparison.
targetEndDate: Column name with end date for comparison.
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.
field: Other columns from the table to intersect.
nameStyle: naming of the added column or columns, should include required parameters.

Value

table with added columns with intersect information.

Examples

# \donttest{
cdm <- mockPatientProfiles()

cdm$cohort1 %>%
  addTableIntersect(tableName = "visit_occurrence")
#> Warning: `addTableIntersect()` was deprecated in PatientProfiles 0.6.0.
#> please use the specific functions instead:
#> • addTableIntersectFlag()
#> • addTableIntersectCount()
#> • addTableIntersectDate()
#> • addTableIntersectDays()
#> # Source:   table<og_173_1715428984> [2 x 8]
#> # Database: DuckDB v0.10.2 [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 4 more variables: visit_occurrence_flag_0_to_inf <dbl>,
#> #   visit_occurrence_count_0_to_inf <dbl>,
#> #   visit_occurrence_date_0_to_inf <date>, visit_occurrence_days_0_to_inf <dbl>
CDMConnector::cdmDisconnect(cdm = cdm)
# }