Package index • DrugUtilisation

Generate a set of drug cohorts

Generate a set of drug cohorts using given concepts or vocabulary hierarchies

generateDrugUtilisationCohortSet(): Generate a set of drug cohorts based on given concepts

generateIngredientCohortSet(): Generate a set of drug cohorts based on drug ingredients

generateAtcCohortSet(): Generate a set of drug cohorts based on ATC classification

erafyCohort(): Erafy a cohort_table collapsing records separated gapEra days or less.

cohortGapEra(): Get the gapEra used to create a cohort

Apply inclusion criteria to drug cohorts

Apply inclusion criteria that filter drug cohort entries based on specified rules.

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

Identify and summarise indications for patients in drug cohorts

Indications identified based on their presence in indication cohorts or OMOP CDM clinical tabes.

addIndication(): Add a variable indicating individuals indications

summariseIndication(): Summarise the indications of individuals in a drug cohort

tableIndication() experimental: Create a table showing indication results

plotIndication(): Generate a plot visualisation (ggplot2) from the output of summariseIndication

Drug use functions

Drug use functions are used to summarise and obtain the drug use information

addDrugUtilisation(): Add new columns with drug use related information

summariseDrugUtilisation(): This function is used to summarise the dose utilisation table over multiple cohorts.

tableDrugUtilisation() experimental: Format a drug_utilisation object into a visual table.

plotDrugUtilisation(): Plot the results of summariseDrugUtilisation

Drug use individual functions

Drug use functions can be used to add a single estimates

addNumberExposures(): To add a new column with the number of exposures. 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.

addTimeToExposure(): To add a new column with the time to exposure. To add multiple columns use addDrugUtilisation() for efficiency.

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.

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.

addCumulativeQuantity(): To add a new column with the cumulative quantity. To add multiple columns use addDrugUtilisation() for efficiency.

addInitialDailyDose(): To add a new column with the initial daily dose. To add multiple columns use addDrugUtilisation() for efficiency.

addCumulativeDose(): To add a new column with the cumulative dose. To add multiple columns use addDrugUtilisation() for efficiency.

Summarise treatment persistence using proportion of patients covered (PPC)

Summarise the proportion of patients in the drug cohort over time.

summariseProportionOfPatientsCovered(): Summarise proportion Of patients covered

tableProportionOfPatientsCovered() experimental: Create a table with proportion of patients covered results

plotProportionOfPatientsCovered(): Plot proportion of patients covered

Summarise treatments during certain windows

Summarise the use of different treatments during certain windows

addTreatment(): Add a variable indicating individuals medications

summariseTreatment(): This function is used to summarise treatments received

tableTreatment() experimental: Format a summarised_treatment result into a visual table.

plotTreatment(): Generate a custom ggplot2 from a summarised_result object generated with summariseTreatment function.

Summarise treatment restart or switch during certain time

Summarise the restart of a treatment, or switch to another, during certain time

addDrugRestart() experimental: Summarise the drug restart per window.

summariseDrugRestart() experimental: Summarise the drug restart per window.

tableDrugRestart() experimental: Format a drug_restart object into a visual table.

plotDrugRestart(): Generate a custom ggplot2 from a summarised_result object generated with summariseDrugRestart() function.

Daily dose documentation

Functions to assess coverage for the diferent ingredients and document how daily dose is calculated

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

summariseDoseCoverage(): Check coverage of daily dose computation in a sample of the cdm for selected concept sets and ingredient

tableDoseCoverage() experimental: Format a dose_coverage object into a visual table.

Complementary functions

Complementary functions

benchmarkDrugUtilisation(): Run benchmark of drug utilisation cohort generation

mockDrugUtilisation(): It creates a mock database for testing DrugUtilisation package

Deprecated functions

This functions has been deprecated

addExposedTime(): To add a new column with the exposed time. To add multiple columns use addDrugUtilisation() for efficiency.

addDailyDose() deprecated: add daily dose information to a drug_exposure table

addRoute() deprecated: add route column to a table containing drug_exposure information

addDrugUse() defunct: Add new columns with drug use related information

summariseDrugUse() defunct: This function is used to summarise the dose table over multiple cohorts.

dailyDoseCoverage() deprecated: Check coverage of daily dose computation in a sample of the cdm for selected concept sets and ingredient

stratifyByUnit() deprecated: Function to stratify a conceptSet by unit

readConceptList() deprecated: Get concept ids from a provided path to json files