generateAtcCohortSet {DrugUtilisation}R Documentation

Generates a cohort of the drug use of ATC name(s) of interest.

Description

Generates a cohort of the drug use of ATC name(s) of interest.

Usage

generateAtcCohortSet(
  cdm,
  name,
  atcName = NULL,
  durationRange = c(1, Inf),
  imputeDuration = "none",
  gapEra = 0,
  priorUseWashout = 0,
  priorObservation = 0,
  cohortDateRange = as.Date(c(NA, NA)),
  limit = "all",
  level = c("ATC 1st"),
  doseForm = NULL
)

Arguments

cdm

A cdm_reference object.

name

Name of the GeneratedCohortSet

atcName

Names of ATC of interest.

durationRange

Range between the duration must be comprised. It should be a numeric vector of length two, with no NAs and the first value should be equal or smaller than the second one. It is only required if imputeDuration = TRUE. If NULL no restrictions are applied.

imputeDuration

Whether/how the duration should be imputed "none", "median", "mean", "mode", or it can be a count

gapEra

Number of days between two continuous exposures to be considered in the same era.

priorUseWashout

Prior days without exposure.

priorObservation

Minimum number of days of prior observation required for the incident eras to be considered.

cohortDateRange

Range for cohort_start_date and cohort_end_date

limit

Choice on how to summarise the exposures. There are two options: "all" we summarise the output will be a summary of the exposed eras of each individual. Each individual can contribute multiple times. "first" we only consider the first observable era of each individual that fulfills the criteria provided in previous parameters. In this case each individual can not contribute with multiple rows.

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.

Value

The function returns the 'cdm' object with the created cohorts as references of the object.

Examples


library(DrugUtilisation)
cdm <- mockDrugUtilisation()
cdm <- generateAtcCohortSet(cdm, name =  "test")
cdm
cdm$test
settings(cdm$test)


[Package DrugUtilisation version 0.6.1 Index]