This function is used to summarise the dose utilisation table over multiple cohorts.

Usage

summariseDrugUtilisation(
  cohort,
  cohortId = NULL,
  strata = list(),
  estimates = c("q25", "median", "q75", "mean", "sd", "count_missing",
    "percentage_missing"),
  ingredientConceptId = NULL,
  conceptSet = NULL,
  indexDate = "cohort_start_date",
  censorDate = "cohort_end_date",
  restrictIncident = TRUE,
  gapEra = 1,
  numberExposures = TRUE,
  numberEras = TRUE,
  daysExposed = TRUE,
  daysPrescribed = TRUE,
  timeToExposure = TRUE,
  initialExposureDuration = TRUE,
  initialQuantity = TRUE,
  cumulativeQuantity = TRUE,
  initialDailyDose = TRUE,
  cumulativeDose = TRUE,
  exposedTime = lifecycle::deprecated()
)

Arguments

cohort: A cohort_table object.
cohortId: A cohort definition id to restrict by. If NULL, all cohorts will be included.
strata: A list of variables to stratify results. These variables must have been added as additional columns in the cohort table.
estimates: Estimates that we want for the columns.
ingredientConceptId: Ingredient OMOP concept that we are interested for the study.
conceptSet: List of concepts to be included.
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.
gapEra: Number of days between two continuous exposures to be considered in the same era.
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).
exposedTime: deprecated.

Value

A summary of drug utilisation stratified by cohort_name and strata_name

Examples

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

cdm <- mockDrugUtilisation()
codelist <- CodelistGenerator::getDrugIngredientCodes(cdm, "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"]] |>
  summariseDrugUtilisation(ingredientConceptId = 1125315)
#> # A tibble: 72 × 13
#>    result_id cdm_name group_name  group_level       strata_name strata_level
#>        <int> <chr>    <chr>       <chr>             <chr>       <chr>       
#>  1         1 DUS MOCK cohort_name 161_acetaminophen overall     overall     
#>  2         1 DUS MOCK cohort_name 161_acetaminophen overall     overall     
#>  3         1 DUS MOCK cohort_name 161_acetaminophen overall     overall     
#>  4         1 DUS MOCK cohort_name 161_acetaminophen overall     overall     
#>  5         1 DUS MOCK cohort_name 161_acetaminophen overall     overall     
#>  6         1 DUS MOCK cohort_name 161_acetaminophen overall     overall     
#>  7         1 DUS MOCK cohort_name 161_acetaminophen overall     overall     
#>  8         1 DUS MOCK cohort_name 161_acetaminophen overall     overall     
#>  9         1 DUS MOCK cohort_name 161_acetaminophen overall     overall     
#> 10         1 DUS MOCK cohort_name 161_acetaminophen overall     overall     
#> # ℹ 62 more rows
#> # ℹ 7 more variables: variable_name <chr>, variable_level <chr>,
#> #   estimate_name <chr>, estimate_type <chr>, estimate_value <chr>,
#> #   additional_name <chr>, additional_level <chr>
# }