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

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

## Documentation for package ‘DrugUtilisation’ version 0.8.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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