addConceptIntersectCount: It creates column to indicate the count overlap information...

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

It creates column to indicate the count overlap information between a table and a concept

Description

It creates column to indicate the count overlap information between a table and a concept

Usage

addConceptIntersectCount(
  x,
  conceptSet,
  indexDate = "cohort_start_date",
  censorDate = NULL,
  window = list(c(0, Inf)),
  targetStartDate = "event_start_date",
  targetEndDate = "event_end_date",
  inObservation = TRUE,
  nameStyle = "{concept_name}_{window_name}",
  name = NULL,
  type = "numeric"
)

Arguments

x	A table containing individuals in a CDM reference.
conceptSet	A named list of concept sets.
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.
targetStartDate	Name or names of start-date columns in the target tables to use for the intersection.
targetEndDate	Name or names of end-date columns in the target tables to use for the intersection. If NULL, the target is treated as a point event.
inObservation	If TRUE, only records that occur during an observation period are considered.
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

The original table (x) with one added column per intersection with the desired conceptSet in a specific window. One column will be created for each combination of window and conceptSet. The value of the column will be the number of intersections in the desired window, or NA if the individual is not in observation at any time in the window.

Examples

library(PatientProfiles)
library(omopgenerics, warn.conflicts = TRUE)
library(dplyr, warn.conflicts = TRUE)

cdm <- mockPatientProfiles(source = "duckdb")

concept <- tibble(
  concept_id = c(1125315),
  domain_id = "Drug",
  vocabulary_id = NA_character_,
  concept_class_id = "Ingredient",
  standard_concept = "S",
  concept_code = NA_character_,
  valid_start_date = as.Date("1900-01-01"),
  valid_end_date = as.Date("2099-01-01"),
  invalid_reason = NA_character_
) |>
  mutate(concept_name = paste0("concept: ", .data$concept_id))
cdm <- insertTable(cdm, "concept", concept)

cdm$cohort1 |>
  addConceptIntersectCount(conceptSet = list("acetaminophen" = 1125315))

PatientProfiles documentation built on Aug. 22, 2026, 1:07 a.m.