Package: DrugExposureDiagnostics 1.1.9

Ger Inberg

DrugExposureDiagnostics: Diagnostics for OMOP Common Data Model Drug Records

Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.

Authors:Ger Inberg [aut, cre], Edward Burn [aut], Theresa Burkard [aut], Yuchen Guo [ctb], Marti Catala [ctb], Mike Du [ctb], Xintong Li [ctb], Ross Williams [ctb], Erasmus MC [cph]

DrugExposureDiagnostics_1.1.9.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DrugExposureDiagnostics/json (API)

# Install 'DrugExposureDiagnostics' in R:

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

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

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

On CRAN:

6.81 score 4 stars 54 scripts 896 downloads 8 exports 49 dependencies

Last updated from:e386f3bb21. Checks:9 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
linux-devel-x86_64	OK	318
source / vignettes	OK	259
linux-release-x86_64	OK	304
macos-release-arm64	OK	155
macos-oldrel-arm64	OK	196
windows-devel	OK	278
windows-release	OK	253
windows-oldrel	OK	264
wasm-release	OK	185

Exports:%>%dataPlotPanel executeChecks metaDataPanel mockDrugExposure runBenchmarkExecuteSingleIngredient viewResults writeResultToDisk

Dependencies:askpass backports bit bit64 blob CDMConnector checkmate cli clipr clock CodelistGenerator cpp11 crayon curl DBI dbplyr dplyr DrugUtilisation generics glue hms httr2 jsonlite lifecycle magrittr omopgenerics openssl PatientProfiles pillar pkgconfig prettyunits progress purrr R6 rappdirs readr rlang snakecase stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr

Introduction To DrugExposureDiagnostics

Drug(s) of interest | Running the diagnostics | Assessing the drug concepts (of interest) | Saving the diagnostic output | View results in the Shiny app & make it available for publishing

Rendered fromIntroductionToDrugExposureDiagnostics.Rmdusingknitr::rmarkdown

Last update: 2026-06-19
Started: 2024-01-15

Run the days supply check | Days supply Overall | Days supply by drug concept

Rendered fromDaysSupply.Rmdusingknitr::rmarkdown

Last update: 2025-02-03
Started: 2024-06-12

Diagnostics Summary

Obtain a diagnostics summary

Rendered fromDiagnosticsSummary.Rmdusingknitr::rmarkdown

Last update: 2025-02-03
Started: 2024-06-12

Run the Drug Dose check | Drug dose

Rendered fromDrugDose.Rmdusingknitr::rmarkdown

Last update: 2025-02-03
Started: 2024-06-12

Run duration check | Drug exposure duration Overall | Drug exposure duration by drug concept

Rendered fromDrugDuration.Rmdusingknitr::rmarkdown

Last update: 2025-02-03
Started: 2024-06-12

Run the Sig checks | Sig | Sig by concept

Rendered fromDrugSig.Rmdusingknitr::rmarkdown

Last update: 2025-02-03
Started: 2024-06-12

Drug Source Concepts

Run checks | Drug Source by Concept

Rendered fromDrugSourceConcepts.Rmdusingknitr::rmarkdown

Last update: 2025-02-03
Started: 2024-06-12

Run the drug type check | Drug Type Overall | Drug Type by drug concept

Rendered fromDrugTypes.Rmdusingknitr::rmarkdown

Last update: 2025-02-03
Started: 2024-06-12

Run missingness check | Overall missingness | Missingness by drug concept

Rendered fromMissingness.Rmdusingknitr::rmarkdown

Last update: 2025-02-03
Started: 2024-06-12

Run the quantity check | Quantity Overall | Quantity by concept

Rendered fromQuantity.Rmdusingknitr::rmarkdown

Last update: 2025-02-03
Started: 2024-06-12

Run the route check | Route Overall | Route by drug concept

Rendered fromRoutes.Rmdusingknitr::rmarkdown

Last update: 2025-02-03
Started: 2024-06-12

Verbatim End Date

Run the Verbatim End Date check | Drug verbatim end date Overall | Drug verbatim end date by concept

Rendered fromVerbatimEndDate.Rmdusingknitr::rmarkdown

Last update: 2025-02-03
Started: 2024-06-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check if Days_supply is the same as datediff(drug_exp_start_date,drug_exp_end_date)	checkDaysSupply
Check the database type.	checkDbType
Get a summary of the daily drug dose	checkDrugDose
Check the drug sig field; this is the verbatim instruction for the drug as written by the provider.	checkDrugSig
Check ingredient is present in given table	checkIngredientInTable
Check is an ingredient	checkIsIngredient
Check if given object is a boolean.	checkLogical
Check that the sample is bigger than the mincellcount	checkSampleMinCellCount
Check if given table exists in cdm.	checkTableExists
Check the verbatim_end_date field	checkVerbatimEndDate
Store the given input in a remote database table. It will be stored either in a permanent table or a temporary table depending on tablePrefix.	computeDBQuery
dataPlotPanel	dataPlotPanel
Execute given checks on Drug Exposure.	executeChecks
Execute given checks on Drug Exposure for a single ingredient.	executeChecksSingleIngredient
Get all options that can be passed to the "checks" parameter	getAllCheckOptions
Check missings in drug exposure records	getDrugMissings
Drug exposure records for ingredients of interest	getDrugRecords
Get drug exposure route types	getDrugRoutes
Check drug exposure source types	getDrugSourceConcepts
Get drug exposure record types	getDrugTypes
Compute the difference in days between 2 variables in a database table.	getDuration
Get the descendants for the given ingredients	ingredientDescendantsInDb
Determine change in memory from running code	mem_change
How much memory is currently used by R?	mem_used
metaDataPanel	metaDataPanel
Mock Drug exposure tables for ingredients of interest	mockDrugExposure
Obscure the small number of counts	obscureCounts
Print duration from start to now and print it as well as new status message	printDurationAndMessage
Run benchmark for ExecuteSingleIngredient	runBenchmarkExecuteSingleIngredient
DrugExposureDiagnostics ShinyApp	ShinyApp
Module Decorator Class	ShinyModule
Create a summary about the diagnostics results	summariseChecks
Summarise drug exposure record durations	summariseDrugExposureDuration
Summarise the quantity column of the drug_exposure table	summariseQuantity
Check time in between drug records per person and report the summary	summariseTimeBetween
Validate the "checks" parameter	validateChecks
View the results in the Shiny app	viewResults
Write a result to a file on disk.	writeFile
Write (ingredient) diagnostics results on disk in given output folder.	writeIngredientResultToDisk
Write diagnostics results to a zip file on disk in given output folder.	writeResultToDisk
Write (ingredient) diagnostics results on disk in given output folder.	writeZipToDisk

Usage by other packages (reverse dependencies)