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
)

Arguments

x	Table with individuals in the cdm.
conceptSet	Concept set list.
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.
targetStartDate	Event start date to use for the intersection.
targetEndDate	Event end date to use for the intersection.
inObservation	If TRUE only records inside an observation period will be considered.
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 overlap information

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$concept_id))
cdm <- CDMConnector::insertTable(cdm, "concept", concept)
result <- cdm$cohort1 %>%
  addConceptIntersectCount(
    conceptSet = list("acetaminophen" = 1125315)
  ) %>%
  dplyr::collect()
mockDisconnect(cdm = cdm)

PatientProfiles documentation built on Oct. 30, 2024, 9:13 a.m.