summariseIndication: Summarise the indications of individuals in a drug cohort

In DrugUtilisation: Summarise Patient-Level Drug Utilisation in Data Mapped to the OMOP Common Data Model

Summarise the indications of individuals in a drug cohort

Description

Summarise the observed indications of patients in a drug cohort based on their presence in an indication cohort in a specified time window. If an individual is not in one of the indication cohorts, they will be considered to have an unknown indication if they are present in one of the specified OMOP CDM clinical tables. Otherwise, if they are neither in an indication cohort or a clinical table they will be considered as having no observed indication.

Usage

summariseIndication(
  cohort,
  strata = list(),
  indicationCohortName,
  cohortId = NULL,
  indicationCohortId = NULL,
  indicationWindow = list(c(0, 0)),
  unknownIndicationTable = NULL,
  indexDate = "cohort_start_date",
  mutuallyExclusive = TRUE,
  censorDate = NULL
)

Arguments

cohort	A cohort_table object.
strata	A list of variables to stratify results. These variables must have been added as additional columns in the cohort table.
indicationCohortName	Name of the cohort table with potential indications.
cohortId	A cohort definition id to restrict by. If NULL, all cohorts will be included.
indicationCohortId	The target cohort ID to add indication. If NULL all cohorts will be considered.
indicationWindow	The time window over which to identify indications.
unknownIndicationTable	Tables in the OMOP CDM to search for unknown indications.
indexDate	Name of a column that indicates the date to start the analysis.
mutuallyExclusive	Whether to report indications as mutually exclusive or report them as independent results.
censorDate	Name of a column that indicates the date to stop the analysis, if NULL end of individuals observation is used.

Value

A summarised result

Examples

library(DrugUtilisation)
library(CDMConnector)
library(dplyr, warn.conflicts = FALSE)

cdm <- mockDrugUtilisation()

indications <- list(headache = 378253, asthma = 317009)
cdm <- generateConceptCohortSet(cdm = cdm,
                                conceptSet = indications,
                                name = "indication_cohorts")

cdm <- generateIngredientCohortSet(cdm = cdm,
                                   name = "drug_cohort",
                                   ingredient = "acetaminophen")

cdm$drug_cohort |>
  summariseIndication(
    indicationCohortName = "indication_cohorts",
    unknownIndicationTable = "condition_occurrence",
    indicationWindow = list(c(-Inf, 0))
  ) |>
  glimpse()

DrugUtilisation documentation built on July 3, 2025, 1:08 a.m.