DrugUtilisation (version 0.8.3)

addIndication: Add a variable indicating individuals indications

Description

Add a variable to a drug cohort indicating 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. If they are neither in an indication cohort or a clinical table they will be considered as having no observed indication.

Usage

addIndication(
  cohort,
  indicationCohortName,
  indicationCohortId = NULL,
  indicationWindow = list(c(0, 0)),
  unknownIndicationTable = NULL,
  indexDate = "cohort_start_date",
  censorDate = NULL,
  mutuallyExclusive = TRUE,
  nameStyle = NULL,
  name = NULL
)

Value

The original table with a variable added that summarises the individual´s indications.

Arguments

cohort

A cohort_table object.

indicationCohortName

Name of indication cohort table

indicationCohortId

target cohort Id to add indication

indicationWindow

time window of interests

unknownIndicationTable

Tables to search unknown indications

indexDate

Name of a column that indicates the date to start the analysis.

censorDate

Name of a column that indicates the date to stop the analysis, if NULL end of individuals observation is used.

mutuallyExclusive

Whether to consider mutually exclusive categories (one column per window) or not (one column per window and indication).

nameStyle

Name style for the indications. By default: 'indication_{window_name}' (mutuallyExclusive = TRUE), 'indication_{window_name}_{cohort_name}' (mutuallyExclusive = FALSE).

name

Name of the new computed cohort table, if NULL a temporary table will be created.

Examples

# \donttest{
library(DrugUtilisation)
library(CDMConnector)
library(dplyr)

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 |>
  addIndication(
    indicationCohortName = "indication_cohorts",
    indicationWindow = list(c(0, 0)),
    unknownIndicationTable = "condition_occurrence"
  ) |>
  glimpse()
# }