Package: DrugUtilisation 1.1.0

Martí Català

DrugUtilisation: Summarise Patient-Level Drug Utilisation in Data Mapped to the OMOP Common Data Model

Summarise patient-level drug utilisation cohorts using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. New users and prevalent users cohorts can be generated and their characteristics, indication and drug use summarised.

Authors:Martí Català [aut, cre], Mike Du [ctb], Yuchen Guo [aut], Kim Lopez-Guell [aut], Edward Burn [aut], Xintong Li [ctb], Marta Alcalde-Herraiz [ctb], Nuria Mercade-Besora [aut], Xihang Chen [aut]

DrugUtilisation_1.1.0.tar.gz
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DrugUtilisation_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DrugUtilisation/json (API)
NEWS

# Install 'DrugUtilisation' in R:

install.packages('DrugUtilisation', repos = c('https://darwin-eu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/darwin-eu/drugutilisation/issues

Pkgdown/docs site:https://darwin-eu.github.io

Datasets:

patternsWithFormula - Patterns valid to compute daily dose with the associated formula.

On CRAN:

8.08 score 3 packages 224 scripts 784 downloads 57 exports 30 dependencies

Last updated from:88bc7cb7f9. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	254
source / vignettes	OK	313
linux-release-x86_64	OK	261
macos-release-arm64	OK	235
macos-oldrel-arm64	OK	249
windows-devel	OK	221
windows-release	OK	203
windows-oldrel	OK	195
wasm-release	OK	187

Exports:addCumulativeDose addCumulativeQuantity addDailyDose addDaysExposed addDaysPrescribed addDrugRestart addDrugUtilisation addIndication addInitialDailyDose addInitialExposureDuration addInitialQuantity additionalColumns addNumberEras addNumberExposures addTimeToExposure addTreatment attrition benchmarkDrugUtilisation bind cohortCodelist cohortCount cohortGapEra erafyCohort exportSummarisedResult generateAtcCohortSet generateDrugUtilisationCohortSet generateIngredientCohortSet groupColumns importSummarisedResult mockDrugUtilisation patternTable plotDrugRestart plotDrugUtilisation plotIndication plotProportionOfPatientsCovered plotTreatment requireDrugInDateRange requireIsFirstDrugEntry requireObservationBeforeDrug requirePriorDrugWashout settings settingsColumns strataColumns summariseDoseCoverage summariseDrugRestart summariseDrugUtilisation summariseIndication summariseProportionOfPatientsCovered summariseTreatment suppress tableDoseCoverage tableDrugRestart tableDrugUtilisation tableIndication tableProportionOfPatientsCovered tableTreatment tidy

Dependencies:blob cli clock CodelistGenerator cpp11 DBI dbplyr dplyr generics glue jsonlite lifecycle magrittr omopgenerics PatientProfiles pillar pkgconfig purrr R6 rlang snakecase stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs withr

Getting drug utilisation related information of subjects in a cohort

Rendered fromdrug_utilisation.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2025-11-19
Started: 2024-07-17

Creating drug cohorts

Rendered fromcreate_cohorts.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2025-11-19
Started: 2024-07-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
To add a new column with the cumulative dose. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addCumulativeDose
To add a new column with the cumulative quantity. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addCumulativeQuantity
Add daily dose to 'drug_exposure' like table	addDailyDose
To add a new column with the days exposed. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addDaysExposed
To add a new column with the days prescribed. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addDaysPrescribed
Add drug restart information as a column per follow-up period of interest.	addDrugRestart
Add new columns with drug use related information	addDrugUtilisation
Add a variable indicating individuals indications	addIndication
To add a new column with the initial daily dose. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addInitialDailyDose
To add a new column with the duration of the first exposure. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addInitialExposureDuration
To add a new column with the initial quantity. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addInitialQuantity
To add a new column with the number of eras. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addNumberEras
To add a new column with the number of exposures. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addNumberExposures
To add a new column with the time to exposure. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addTimeToExposure
Add a variable indicating individuals medications	addTreatment
Run benchmark of drug utilisation cohort generation	benchmarkDrugUtilisation
Get the gapEra used to create a cohort	cohortGapEra
Erafy a cohort_table collapsing records separated gapEra days or less.	erafyCohort
Generate a set of drug cohorts based on ATC classification	generateAtcCohortSet
Generate a set of drug cohorts based on given concepts	generateDrugUtilisationCohortSet
Generate a set of drug cohorts based on drug ingredients	generateIngredientCohortSet
It creates a mock database for testing DrugUtilisation package	mockDrugUtilisation
Patterns valid to compute daily dose with the associated formula.	patternsWithFormula
Function to create a tibble with the patterns from current drug strength table	patternTable
Generate a custom ggplot2 from a summarised_result object generated with summariseDrugRestart() function.	plotDrugRestart
Plot the results of 'summariseDrugUtilisation'	plotDrugUtilisation
Generate a plot visualisation (ggplot2) from the output of summariseIndication	plotIndication
Plot proportion of patients covered	plotProportionOfPatientsCovered
Generate a custom ggplot2 from a summarised_result object generated with summariseTreatment function.	plotTreatment
Restrict cohort to only cohort records within a certain date range	requireDrugInDateRange
Restrict cohort to only the first cohort record per subject	requireIsFirstDrugEntry
Restrict cohort to only cohort records with the given amount of prior observation time in the database	requireObservationBeforeDrug
Restrict cohort to only cohort records with a given amount of time since the last cohort record ended	requirePriorDrugWashout
Check coverage of daily dose computation in a sample of the cdm for selected concept sets and ingredient	summariseDoseCoverage
Summarise the drug restart for each follow-up period of interest.	summariseDrugRestart
This function is used to summarise the dose utilisation table over multiple cohorts.	summariseDrugUtilisation
Summarise the indications of individuals in a drug cohort	summariseIndication
Summarise proportion Of patients covered	summariseProportionOfPatientsCovered
This function is used to summarise treatments received	summariseTreatment
Format a dose_coverage object into a visual table.	tableDoseCoverage
Format a drug_restart object into a visual table.	tableDrugRestart
Format a drug_utilisation object into a visual table.	tableDrugUtilisation
Create a table showing indication results	tableIndication
Create a table with proportion of patients covered results	tableProportionOfPatientsCovered
Format a summarised_treatment result into a visual table.	tableTreatment