Intersecting the cohort with columns of an OMOP table of user's choice. It will add an extra column to the cohort, indicating the intersected entries with the target columns in a window of the user's choice.

Usage

addTableIntersectField(
  x,
  tableName,
  field,
  indexDate = "cohort_start_date",
  censorDate = NULL,
  window = list(c(0, Inf)),
  targetDate = startDateColumn(tableName),
  order = "first",
  nameStyle = "{table_name}_{extra_value}_{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.
field: The columns from the table in tableName to intersect over. For example, if the user uses visit_occurrence in tableName then for field the possible options include visit_occurrence_id, visit_concept_id, visit_type_concept_id.
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 when intersecting with the chosen column.
targetDate: The dates in the target columns in tableName that the user may want to restrict to.
order: which record is considered in case of multiple records (only required for date and days options).
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.

Value

table with added columns with intersect information.

Examples

# \donttest{
cdm <- mockPatientProfiles()
cdm$cohort1 %>%
  addTableIntersectField(
    tableName = "visit_occurrence",
    field = "visit_concept_id",
    order = "last",
    window = c(-Inf, -1)
  )
#> # Source:   table<og_159_1730219878> [10 x 5]
#> # Database: DuckDB v1.1.1 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:]
#>    cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                   <int>      <int> <date>            <date>         
#>  1                    3          5 1993-04-14        1994-06-18     
#>  2                    1          2 2010-11-18        2011-08-04     
#>  3                    2         10 1956-05-20        1958-04-22     
#>  4                    2          9 1960-08-12        1964-11-18     
#>  5                    3          7 1957-05-26        1958-09-29     
#>  6                    1          1 1932-07-13        1934-01-27     
#>  7                    3          6 1958-10-10        1964-03-03     
#>  8                    2          4 1937-11-10        1946-04-03     
#>  9                    3          3 1926-09-19        1931-01-16     
#> 10                    3          8 1966-09-15        1987-03-22     
#> # ℹ 1 more variable: visit_occurrence_visit_concept_id_minf_to_m1 <chr>
mockDisconnect(cdm = cdm)
# }