addConceptIntersectField: It adds a custom column (field) from the intersection with a...

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

It adds a custom column (field) from the intersection with a certain table subsetted by concept id. In general it is used to add the first value of a certain measurement.

Description

It adds a custom column (field) from the intersection with a certain table subsetted by concept id. In general it is used to add the first value of a certain measurement.

Usage

addConceptIntersectField(
  x,
  conceptSet,
  field,
  indexDate = "cohort_start_date",
  censorDate = NULL,
  window = list(c(0, Inf)),
  targetDate = "event_start_date",
  order = "first",
  inObservation = TRUE,
  allowDuplicates = FALSE,
  nameStyle = "{field}_{concept_name}_{window_name}",
  name = NULL
)

Arguments

x	Table with individuals in the cdm.
conceptSet	Concept set list.
field	Column in the standard omop table that you want to add.
indexDate	Variable in x that contains the date to compute the intersection.
censorDate	Whether to censor overlap events at a date column of x
window	Window to consider events in.
targetDate	Event date to use for the intersection.
order	'last' or 'first' to refer to which event consider if multiple events are present in the same window.
inObservation	If TRUE only records inside an observation period will be considered.
allowDuplicates	Whether to allow multiple records with same conceptSet, person_id and targetDate. If switched to TRUE, it can have a different and unpredictable behavior depending on the cdm_source.
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 the 'field' value obtained from the intersection

Examples

library(PatientProfiles)
cdm <- mockPatientProfiles()
concept <- dplyr::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_
) |>
  dplyr::mutate(concept_name = paste0("concept: ", .data$concept_id))
cdm <- CDMConnector::insertTable(cdm, "concept", concept)

cdm$cohort1 |>
  addConceptIntersectField(
    conceptSet = list("acetaminophen" = 1125315),
    field = "drug_type_concept_id"
  )

mockDisconnect(cdm = cdm)

PatientProfiles documentation built on April 3, 2025, 9:47 p.m.