Package: DrugUtilisation 1.2.1

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_1.2.1.tar.gz
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DrugUtilisation_1.2.1.tgz(r-4.6-any)DrugUtilisation_1.2.1.tgz(r-4.5-any)
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DrugUtilisation_1.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DrugUtilisation/json (API)

# 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:

On CRAN:

Conda:

8.00 score 3 packages 187 scripts 960 downloads 60 exports 30 dependencies

Last updated from:88e3a515db. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK306
source / vignettesOK309
linux-release-x86_64OK297
macos-release-arm64OK168
macos-oldrel-arm64OK173
windows-develOK228
windows-releaseOK229
windows-oldrelOK227
wasm-releaseOK194

Exports:addCumulativeDoseaddCumulativeQuantityaddDailyDoseaddDaysExposedaddDaysPrescribedaddDrugRestartaddDrugUtilisationaddIndicationaddInitialDailyDoseaddInitialExposureDurationaddInitialQuantityadditionalColumnsaddNumberErasaddNumberExposuresaddTimeToExposureaddTreatmentattritionbenchmarkDrugUtilisationbindcohortCodelistcohortCountcohortGapEraerafyCohortexportSummarisedResultgenerateAtcCohortSetgenerateDrugUtilisationCohortSetgenerateIngredientCohortSetgroupColumnsimportSummarisedResultmockDrugUtilisationpatternTableplotDiscontinuationAsSurvivalplotDrugRestartplotDrugUtilisationplotIndicationplotProportionOfPatientsCoveredplotTreatmentrequireDrugInDateRangerequireIsFirstDrugEntryrequireObservationBeforeDrugrequirePriorDrugWashoutsettingssettingsColumnsstrataColumnssummariseDiscontinuationAsSurvivalsummariseDoseCoveragesummariseDrugRestartsummariseDrugUtilisationsummariseIndicationsummariseProportionOfPatientsCoveredsummariseTreatmentsuppresstableDiscontinuationAsSurvivaltableDoseCoveragetableDrugRestarttableDrugUtilisationtableIndicationtableProportionOfPatientsCoveredtableTreatmenttidy

Dependencies:blobcliclockCodelistGeneratorcpp11DBIdbplyrdplyrgenericsgluejsonlitelifecyclemagrittromopgenericsPatientProfilespillarpkgconfigpurrrR6rlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrswithr

Getting drug utilisation related information of subjects in a cohort
Introduction | Set up | Mock data | Drug codes | Add drug utilisation information | addNumberExposures() | addNumberEras() | daysExposed | daysPrescribed | timeToExposure | initialExposureDuration | initialQuantity and cumulativeQuantity | initialDailyDose and cumulativeDose | addDrugUtilisation() | Use case | Summarise drug utilisation information | summariseDrugUtilisation() | tableDrugUtilisation()
Rendered fromdrug_utilisation.Rmdusingknitr::rmarkdown

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

Creating drug cohorts
Introduction | Creating a cdm_reference object | Create a drug users cohort | Creating a conceptSet | The gapEra parameter | Create your cohort | Analogous functions | Carry over days / Use days prescribed | Apply inclusion criteria to drug cohorts | requirePriorDrugWashout() | requireIsFirstDrugEntry() | requireObservationBeforeDrug() | requireDrugInDateRange() | The order matters | first and washout | first and minObs | first and 2011-2012 | washout and minObs | washout and 2011-2012 | minObs and 2011-2012 | Recommended order
Rendered fromcreate_cohorts.Rmdusingknitr::rmarkdown

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

Readme and manuals

Help Manual

Help pageTopics
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 tableaddDailyDose
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 informationaddDrugUtilisation
Add a variable indicating individuals indicationsaddIndication
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 medicationsaddTreatment
Run benchmark of drug utilisation cohort generationbenchmarkDrugUtilisation
Get the gapEra used to create a cohortcohortGapEra
Erafy a cohort_table collapsing records separated gapEra days or less.erafyCohort
Generate a set of drug cohorts based on ATC classificationgenerateAtcCohortSet
Generate a set of drug cohorts based on given conceptsgenerateDrugUtilisationCohortSet
Generate a set of drug cohorts based on drug ingredientsgenerateIngredientCohortSet
It creates a mock database for testing DrugUtilisation packagemockDrugUtilisation
Patterns valid to compute daily dose with the associated formula.patternsWithFormula
Function to create a tibble with the patterns from current drug strength tablepatternTable
Plot discontinuationplotDiscontinuationAsSurvival
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 summariseIndicationplotIndication
Plot proportion of patients coveredplotProportionOfPatientsCovered
Generate a custom ggplot2 from a summarised_result object generated with summariseTreatment function.plotTreatment
Restrict cohort to only cohort records within a certain date rangerequireDrugInDateRange
Restrict cohort to only the first cohort record per subjectrequireIsFirstDrugEntry
Restrict cohort to only cohort records with the given amount of prior observation time in the databaserequireObservationBeforeDrug
Restrict cohort to only cohort records with a given amount of time since the last cohort record endedrequirePriorDrugWashout
Summarise discontinuation as a survival analysissummariseDiscontinuationAsSurvival
Check coverage of daily dose computation in a sample of the cdm for selected concept sets and ingredientsummariseDoseCoverage
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 cohortsummariseIndication
Summarise proportion Of patients coveredsummariseProportionOfPatientsCovered
This function is used to summarise treatments receivedsummariseTreatment
Create a table with discontinuation as survival resultstableDiscontinuationAsSurvival
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 resultstableIndication
Create a table with proportion of patients covered resultstableProportionOfPatientsCovered
Format a summarised_treatment result into a visual table.tableTreatment