summariseDrugUtilisation {DrugUtilisation} | R Documentation |
This function is used to summarise the dose utilisation table over multiple cohorts.
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
)
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. |
A summary of drug utilisation stratified by cohort_name and strata_name
library(DrugUtilisation)
library(CodelistGenerator)
cdm <- mockDrugUtilisation()
codelist <- CodelistGenerator::getDrugIngredientCodes(cdm, "acetaminophen")
cdm <- generateDrugUtilisationCohortSet(
cdm, "dus_cohort", codelist
)
cdm[["dus_cohort"]] %>%
summariseDrugUtilisation(ingredientConceptId = 1125315)