Generate a set of drug cohorts based on ATC classification

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,
  gapEra = 1,
  subsetCohort = NULL,
  subsetCohortId = NULL,
  numberExposures = FALSE,
  daysPrescribed = FALSE,
  ...,
  durationRange = lifecycle::deprecated(),
  imputeDuration = lifecycle::deprecated(),
  priorUseWashout = lifecycle::deprecated(),
  priorObservation = lifecycle::deprecated(),
  cohortDateRange = lifecycle::deprecated(),
  limit = lifecycle::deprecated()
)

Arguments

cdm

A cdm_reference object.

name

Name of the new cohort table, it must be a length 1 character vector.

atcName

Names of ATC classification of interest.

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.

subsetCohort

Cohort table to subset.

subsetCohortId

Cohort id to subset.

numberExposures

Whether to include 'number_exposures' (number of drug exposure records between indexDate and censorDate).

daysPrescribed

Whether to include 'days_prescribed' (number of days prescribed used to create each era).

...

Arguments to be passed to CodelistGenerator::getATCCodes().

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

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

cdm <- mockDrugUtilisation()

cdm <- generateAtcCohortSet(
  cdm = cdm,
  atcName = "alimentary tract and metabolism",
  name = "drugs"
)
#> ℹ Subsetting drug_exposure table
#> ℹ Checking whether any record needs to be dropped.
#> ℹ Collapsing overlaping records.
#> Warning: cohort_name must be snake case and have less than 100 characters, the following
#> cohorts will be renamed:
#> • alimentary tract and metabolism -> alimentary_tract_and_metabolism
#> ℹ Collapsing records with gapEra = 1 days.

cdm$drugs |>
  glimpse()
#> Rows: ??
#> Columns: 6
#> Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#> $ cohort_definition_id <int> 
#> $ subject_id           <int> 
#> $ cohort_start_date    <date> 
#> $ cohort_end_date      <date> 
#> $ number_exposures     <int> 
#> $ days_prescribed      <int> 
# }