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}"
)

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.
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.

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_146_1715898477> [10 x 5]
#> # Database: DuckDB v0.10.2 [unknown@Linux 6.5.0-1021-azure:R 4.4.0/:memory:]
#>    cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                   <int>      <int> <date>            <date>         
#>  1                    2          9 2018-03-25        2041-06-14     
#>  2                    3          2 2067-11-18        2111-03-13     
#>  3                    1          7 1975-10-22        2047-09-18     
#>  4                    3          1 1943-10-07        1944-09-20     
#>  5                    2          5 2008-08-30        2063-02-08     
#>  6                    1         10 1944-02-07        1984-11-09     
#>  7                    1          4 2039-03-04        2048-12-13     
#>  8                    2          6 2092-08-12        2161-12-28     
#>  9                    1          3 1959-08-02        1999-10-22     
#> 10                    2          8 1991-01-08        1992-10-05     
#> # ℹ 1 more variable: visit_occurrence_visit_concept_id_minf_to_m1 <chr>
mockDisconnect(cdm = cdm)
# }