generateAtcCohortSet {DrugUtilisation}

Generate a set of drug cohorts based on ATC classification

Description

Adds a new cohort table to the cdm reference with individuals who have drug exposure records that belong to the specified Anatomical Therapeutic Chemical (ATC) classification. Cohort start and end dates will be based on drug record start and end dates, respectively. Records that overlap or have fewer days between them than the specified gap era will be concatenated into a single cohort entry.

Usage

generateAtcCohortSet(
  cdm,
  name,
  atcName = NULL,
  level = c("ATC 1st"),
  doseForm = NULL,
  gapEra = 1,
  durationRange = lifecycle::deprecated(),
  imputeDuration = lifecycle::deprecated(),
  priorUseWashout = lifecycle::deprecated(),
  priorObservation = lifecycle::deprecated(),
  cohortDateRange = lifecycle::deprecated(),
  limit = lifecycle::deprecated()
)

Arguments

cdm

A cdm reference.

name

The name of the new cohort table to add to the cdm reference.

atcName

Names of ATC classification of interest.

level

ATC level. Can be one or more of "ATC 1st", "ATC 2nd", "ATC 3rd", "ATC 4th", and "ATC 5th"

doseForm

Only descendants codes with the specified dose form will be returned. If NULL, descendant codes will be returned regardless of dose form.

gapEra

Number of days between two continuous exposures to be considered in the same era. Records that have fewer days between them than this gap will be concatenated into the same cohort record.

durationRange

Deprecated.

imputeDuration

Deprecated.

priorUseWashout

Deprecated

priorObservation

Deprecated.

cohortDateRange

Deprecated.

limit

Deprecated.

Value

The function returns the cdm reference provided with the addition of the new cohort table.

Examples

library(DrugUtilisation)
library(dplyr)

cdm <- mockDrugUtilisation()

cdm <- generateAtcCohortSet(
  cdm = cdm,
  atcName = "alimentary tract and metabolism",
  name = "drugs"
)

cdm$drugs |>
  glimpse()