addTableIntersectField: Intersecting the cohort with columns of an OMOP table of...

In PatientProfiles: Identify Characteristics of Patients in the OMOP Common Data Model

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.

Description

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),
  inObservation = TRUE,
  order = "first",
  allowDuplicates = FALSE,
  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.
inObservation	If TRUE only records inside an observation period will be considered.
order	which record is considered in case of multiple records (only required for date and days options).
allowDuplicates	Whether to allow multiple records with same conceptSet, person_id and targetDate. If switched to TRUE, the created new columns (field) will be collapsed to a character vector separated by ';' to account for multiple values per person.
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

library(PatientProfiles)

cdm <- mockPatientProfiles(source = "duckdb")

cdm$cohort1 |>
  addTableIntersectField(
    tableName = "visit_occurrence",
    field = "visit_concept_id",
    order = "last",
    window = c(-Inf, -1)
  )

PatientProfiles documentation built on Nov. 5, 2025, 7:05 p.m.