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This function is used to summarise the dose utilisation table over multiple cohorts.
summariseDrugUtilisation.Rd
This function is used to summarise the dose utilisation table over multiple cohorts.
Usage
summariseDrugUtilisation(
cohort,
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,
exposedTime = TRUE,
timeToExposure = TRUE,
initialQuantity = TRUE,
cumulativeQuantity = TRUE,
initialDailyDose = TRUE,
cumulativeDose = TRUE
)
Arguments
- cohort
Cohort with drug use variables and strata.
- strata
Stratification list.
- estimates
Estimates that we want for the columns.
- ingredientConceptId
Ingredient OMOP concept that we are interested for the study. It is a compulsory input, no default value is provided.
- conceptSet
List of concepts to be included. If NULL all the descendants of ingredient concept id will be used.
- 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 add a column with the number of exposures.
- numberEras
Whether to add a column with the number of eras.
- exposedTime
Whether to add a column with the number of exposed days.
- timeToExposure
Whether to add a column with the number of days between indexDate and start of the first exposure.
- initialQuantity
Whether to add a column with the initial quantity.
- cumulativeQuantity
Whether to add a column with the cumulative quantity of the identified prescription.
- initialDailyDose
Whether to add a column with the initial daily dose.
- cumulativeDose
Whether to add a column with the cumulative dose.
Examples
# \donttest{
library(DrugUtilisation)
library(CodelistGenerator)
cdm <- mockDrugUtilisation()
codelist <- CodelistGenerator::getDrugIngredientCodes(cdm, "acetaminophen")
cdm <- generateDrugUtilisationCohortSet(
cdm, "dus_cohort", codelist
)
cdm[["dus_cohort"]] %>%
summariseDrugUtilisation(ingredientConceptId = 1125315)
#> # A tibble: 58 × 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 48 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>
# }