Add new columns with drug use related information

Usage

addDrugUtilisation(
  cohort,
  gapEra,
  conceptSet = NULL,
  ingredientConceptId = NULL,
  indexDate = "cohort_start_date",
  censorDate = "cohort_end_date",
  restrictIncident = TRUE,
  numberExposures = TRUE,
  numberEras = TRUE,
  daysExposed = TRUE,
  daysPrescribed = TRUE,
  timeToExposure = TRUE,
  initialExposureDuration = TRUE,
  initialQuantity = TRUE,
  cumulativeQuantity = TRUE,
  initialDailyDose = TRUE,
  cumulativeDose = TRUE,
  nameStyle = "{value}_{concept_name}_{ingredient}",
  name = NULL,
  exposedTime = lifecycle::deprecated()
)

Arguments

cohort: A cohort_table object.
gapEra: Number of days between two continuous exposures to be considered in the same era.
conceptSet: List of concepts to be included.
ingredientConceptId: Ingredient OMOP concept that we are interested for the study.
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.
restrictIncident: Whether to include only incident prescriptions in the analysis. If FALSE all prescriptions that overlap with the study period will be included.
numberExposures: Whether to include 'number_exposures' (number of drug exposure records between indexDate and censorDate).
numberEras: Whether to include 'number_eras' (number of continuous exposure episodes between indexDate and censorDate).
daysExposed: Whether to include 'days_exposed' (number of days that the individual is in a continuous exposure episode, including allowed treatment gaps, between indexDate and censorDate; sum of the length of the different drug eras).
daysPrescribed: Whether to include 'days_prescribed' (sum of the number of days for each prescription that contribute in the analysis).
timeToExposure: Whether to include 'time_to_exposure' (number of days between indexDate and the first episode).
initialExposureDuration: Whether to include 'initial_exposure_duration' (number of prescribed days of the first drug exposure record).
initialQuantity: Whether to include 'initial_quantity' (quantity of the first drug exposure record).
cumulativeQuantity: Whether to include 'cumulative_quantity' (sum of the quantity of the different exposures considered in the analysis).
initialDailyDose: Whether to include 'initial_daily_dose_{unit}' (daily dose of the first considered prescription).
cumulativeDose: Whether to include 'cumulative_dose_{unit}' (sum of the cumulative dose of the analysed drug exposure records).
nameStyle: Character string to specify the nameStyle of the new columns.
name: Name of the new computed cohort table, if NULL a temporary table will be created.
exposedTime: deprecated.

Value

The same cohort with the added columns.

Examples

# \donttest{
library(DrugUtilisation)

cdm <- mockDrugUtilisation()
codelist <- CodelistGenerator::getDrugIngredientCodes(
  cdm,
  name = "acetaminophen"
)

cdm <- generateDrugUtilisationCohortSet(cdm, "dus_cohort", codelist)
#> 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[["dus_cohort"]] |>
  addDrugUtilisation(ingredientConceptId = 1125315, gapEra = 30)
#> # Source:   table<og_064_1734614264> [?? x 14]
#> # Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#>   cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                  <int>      <int> <date>            <date>         
#> 1                    1          5 2011-03-26        2012-01-07     
#> 2                    1          9 2019-09-07        2019-11-23     
#> 3                    1          7 1982-08-25        1983-06-05     
#> 4                    1          4 2022-02-19        2022-06-03     
#> 5                    1          2 2021-12-21        2021-12-24     
#> 6                    1          7 1985-04-10        1986-11-25     
#> 7                    1         10 2022-11-27        2022-11-30     
#> # ℹ 10 more variables: number_exposures_ingredient_1125315_descendants <int>,
#> #   time_to_exposure_ingredient_1125315_descendants <int>,
#> #   cumulative_quantity_ingredient_1125315_descendants <dbl>,
#> #   initial_quantity_ingredient_1125315_descendants <dbl>,
#> #   initial_exposure_duration_ingredient_1125315_descendants <int>,
#> #   number_eras_ingredient_1125315_descendants <int>,
#> #   days_exposed_ingredient_1125315_descendants <int>, …
# }