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

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Documentation for package ‘DrugUtilisation’ version 0.7.0

• 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
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.
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.
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
defaultTableOptions	Additional arguments for the table functions.
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.
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.