Generate a set of drug cohorts based on drug ingredients — generateIngredientCohortSet • DrugUtilisation

Adds a new cohort table to the cdm reference with individuals who have drug exposure records with the specified drug ingredient. 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

generateIngredientCohortSet(
  cdm,
  name,
  ingredient = 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.
ingredient: Accepts both vectors and named lists of ingredient names. For a vector input, e.g., c("acetaminophen", "codeine"), it generates a cohort table with descendant concept codes for each ingredient, assigning unique cohort_definition_id. For a named list input, e.g., list( "test_1" = c("simvastatin", "acetaminophen"), "test_2" = "metformin"), it produces a cohort table based on the structure of the input, where each name leads to a combined set of descendant concept codes for the specified ingredients, creating distinct cohort_definition_id for each named group.
gapEra: Number of days between two continuous exposures to be considered in the same era.
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::getDrugIngredientCodes().
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 <- generateIngredientCohortSet(
  cdm = cdm,
  ingredient = "acetaminophen",
  name = "acetaminophen"
)
#> ℹ Subsetting drug_exposure table
#> ℹ Checking whether any record needs to be dropped.
#> ℹ Collapsing overlaping records.
#> ℹ Collapsing records with gapEra = 1 days.

cdm$acetaminophen |>
  glimpse()
#> Rows: ??
#> Columns: 4
#> Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#> $ cohort_definition_id <int> 1, 1, 1, 1, 1
#> $ subject_id           <int> 4, 5, 8, 2, 10
#> $ cohort_start_date    <date> 2016-07-15, 1999-07-07, 2017-06-02, 2006-02-08, 2…
#> $ cohort_end_date      <date> 2016-12-05, 1999-07-31, 2017-10-04, 2006-05-19, 2…
# }