Package: DrugUtilisation 0.7.1

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]

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DrugUtilisation.pdf |DrugUtilisation.html✨
DrugUtilisation/json (API)
NEWS

# Install 'DrugUtilisation' in R:

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

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

Datasets:

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

On CRAN:

53 exports 4 stars 2.99 score 51 dependencies 2 dependents 267 scripts 772 downloads

Last updated 8 days agofrom:08f7a3203c. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 10 2024
R-4.5-win	OK	Sep 10 2024
R-4.5-linux	OK	Sep 10 2024
R-4.4-win	OK	Sep 10 2024
R-4.4-mac	OK	Sep 10 2024
R-4.3-win	OK	Sep 10 2024
R-4.3-mac	OK	Sep 10 2024

Exports:addCumulativeDose addCumulativeQuantity addDailyDose addDrugUse addDrugUtilisation addExposedTime addIndication addInitialDailyDose addInitialQuantity addNumberEras addNumberExposures addRoute addTimeToExposure attrition benchmarkDrugUtilisation bind cohortCodelist cohortCount cohortGapEra dailyDoseCoverage defaultTableOptions exportSummarisedResult generateAtcCohortSet generateDrugUtilisationCohortSet generateIngredientCohortSet mockDisconnect mockDrugUtilisation patternTable plotDrugRestart plotIndication plotProportionOfPatientsCovered plotTreatment readConceptList requireDrugInDateRange requireIsFirstDrugEntry requireObservationBeforeDrug requirePriorDrugWashout settings stratifyByUnit summariseDoseCoverage summariseDrugRestart summariseDrugUse summariseDrugUtilisation summariseIndication summariseProportionOfPatientsCovered summariseTreatment suppress tableDoseCoverage tableDrugRestart tableDrugUtilisation tableIndication tableProportionOfPatientsCovered tableTreatment

Dependencies:backports bit bit64 blob CDMConnector checkmate cli clipr clock CodelistGenerator cpp11 crayon DBI dbplyr diffobj dplyr fansi fs generics glue hms jsonlite lifecycle lubridate magrittr omopgenerics PatientProfiles pillar pkgconfig prettyunits progress purrr R6 readr rematch2 RJSONIO rlang snakecase stringi stringr tibble tidyr tidyselect timechange tzdb utf8 vctrs visOmopResults vroom waldo withr

Getting drug utilisation related information of subjects in a cohort

Rendered fromdrug_utilisation.Rmdusingknitr::rmarkdownon Sep 10 2024.

Last update: 2024-07-30
Started: 2024-07-17

Creating drug cohorts

Rendered fromcreate_cohorts.Rmdusingknitr::rmarkdownon Sep 10 2024.

Last update: 2024-07-30
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 information to a drug_exposure table	addDailyDose
Add new columns with drug use related information	addDrugUse
Add new columns with drug use related information	addDrugUtilisation
To add a new column with the exposed time. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addExposedTime
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 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
add route column to a table containing drug_exposure information	addRoute
To add a new column with the time to exposure. To add multiple columns use 'addDrugUtilisation()' for efficiency.	addTimeToExposure
Run benchmark of drug utilisation cohort generation	benchmarkDrugUtilisation
Get the gapEra used to create a cohort	cohortGapEra
Check coverage of daily dose computation in a sample of the cdm for selected concept sets and ingredient	dailyDoseCoverage
Additional arguments for the table functions.	defaultTableOptions
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
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
Get concept ids from a provided path to json files	readConceptList
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
Function to stratify a conceptSet by unit	stratifyByUnit
Check coverage of daily dose computation in a sample of the cdm for selected concept sets and ingredient	summariseDoseCoverage
Summarise the drug restart per window.	summariseDrugRestart
This function is used to summarise the dose table over multiple cohorts.	summariseDrugUse
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