Package: DrugExposureDiagnostics 1.1.1

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_1.1.1.tar.gz
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DrugExposureDiagnostics.pdf |DrugExposureDiagnostics.html✨
DrugExposureDiagnostics/json (API)
NEWS

# 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 site:https://darwin-eu.github.io

On CRAN:

7.07 score 4 stars 41 scripts 392 downloads 8 exports 68 dependencies

Last updated 14 days agofrom:c95828cfe7. Checks:8 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 06 2025
R-4.5-win	OK	Feb 06 2025
R-4.5-mac	OK	Feb 06 2025
R-4.5-linux	OK	Feb 06 2025
R-4.4-win	OK	Feb 06 2025
R-4.4-mac	OK	Feb 06 2025
R-4.3-win	OK	Feb 06 2025
R-4.3-mac	OK	Feb 06 2025

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

Dependencies:backports base64enc bit bit64 blob bslib cachem CDMConnector checkmate cli clipr clock CodelistGenerator commonmark cpp11 crayon DBI dbplyr digest dplyr DrugUtilisation fansi fastmap fontawesome fs generics glue hms htmltools httpuv jquerylib jsonlite later lifecycle lubridate magrittr memoise mime omopgenerics PatientProfiles pillar pkgconfig prettyunits progress promises purrr R6 rappdirs Rcpp readr RJSONIO rlang sass shiny snakecase sourcetools stringi stringr tibble tidyr tidyselect timechange tzdb utf8 vctrs vroom withr xtable

Days Supply

Rendered fromDaysSupply.Rmdusingknitr::rmarkdownon Feb 06 2025.

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

Diagnostics Summary

Rendered fromDiagnosticsSummary.Rmdusingknitr::rmarkdownon Feb 06 2025.

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

Drug Dose

Rendered fromDrugDose.Rmdusingknitr::rmarkdownon Feb 06 2025.

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

DrugDuration

Rendered fromDrugDuration.Rmdusingknitr::rmarkdownon Feb 06 2025.

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

Drug Sig

Rendered fromDrugSig.Rmdusingknitr::rmarkdownon Feb 06 2025.

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

Drug Source Concepts

Rendered fromDrugSourceConcepts.Rmdusingknitr::rmarkdownon Feb 06 2025.

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

Drug Types

Rendered fromDrugTypes.Rmdusingknitr::rmarkdownon Feb 06 2025.

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

Introduction To DrugExposureDiagnostics

Rendered fromIntroductionToDrugExposureDiagnostics.Rmdusingknitr::rmarkdownon Feb 06 2025.

Last update: 2025-02-03
Started: 2024-01-15

Missingness

Rendered fromMissingness.Rmdusingknitr::rmarkdownon Feb 06 2025.

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

Quantity

Rendered fromQuantity.Rmdusingknitr::rmarkdownon Feb 06 2025.

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

Routes

Rendered fromRoutes.Rmdusingknitr::rmarkdownon Feb 06 2025.

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

Verbatim End Date

Rendered fromVerbatimEndDate.Rmdusingknitr::rmarkdownon Feb 06 2025.

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
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
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
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
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)