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}_{field}_{window_name}",
  name = NULL,
  type = "auto"
)

Arguments

x	A table containing individuals in a CDM reference.
tableName	Names of one or more OMOP CDM tables to intersect with.
field	Name or names of columns in the target tables to add to x.
indexDate	Name of a date column in x, or a single date to use for all rows, used as the reference date.
censorDate	Date or name of a date column in x on which to censor follow-up. If NULL, no censoring is applied.
window	Window or windows of time relative to indexDate to consider.
targetDate	Name or names of date columns in the target tables to use for the intersection.
inObservation	If TRUE, only records that occur during an observation period are considered.
order	Which record to use when multiple records occur in a window: "first" or "last".
allowDuplicates	Whether to allow multiple records for the same person, target, and date. If TRUE, multiple values are collapsed into a semicolon-separated character value; otherwise, duplicates result in an error.
nameStyle	Naming pattern for the added column or columns. It should include the required formatting variables. If more than one tableName is provided, it must include {table_name}.
name	Name of the new table. If NULL, a temporary table is returned.
type	Type of the created column(s). Counts, days, age, and observation durations can be "numeric" or "integer". Flag columns can also be "logical". Field columns can use "auto" to preserve the source type, or can be converted to "numeric", "integer", "logical", or "character".

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 Aug. 22, 2026, 1:07 a.m.