_pkgdown.yml

url: https://darwin-eu.github.io/DrugUtilisation/
template:
  bootstrap: 5

articles:
- title: Package functionalities
  navbar: Package functionalities
  contents:
  - mock_data
  - create_cohorts
  - indication
  - daily_dose_calculation
  - drug_utilisation
  - summarise_treatments
  - treatment_discontinuation
  - drug_restart

reference:
- subtitle: Generate a set of drug cohorts
  desc: Generate a set of drug cohorts using given concepts or vocabulary hierarchies
- contents:
  - generateDrugUtilisationCohortSet
  - generateIngredientCohortSet
  - generateAtcCohortSet
  - erafyCohort
  - cohortGapEra
- subtitle: Apply inclusion criteria to drug cohorts
  desc: Apply inclusion criteria that filter drug cohort entries based on specified rules.
- contents:
  - requireDrugInDateRange
  - requireIsFirstDrugEntry
  - requireObservationBeforeDrug
  - requirePriorDrugWashout
- subtitle: Identify and summarise indications for patients in drug cohorts
  desc: Indications identified based on their presence in indication cohorts or OMOP CDM clinical tabes.
- contents:
  - addIndication
  - summariseIndication
  - tableIndication
  - plotIndication
- subtitle: Drug use functions
  desc: Drug use functions are used to summarise and obtain the drug use information
- contents:
  - addDrugUtilisation
  - summariseDrugUtilisation
  - tableDrugUtilisation
  - plotDrugUtilisation
- subtitle: Drug use individual functions
  desc: Drug use functions can be used to add a single estimates
- contents:
  - addNumberExposures
  - addNumberEras
  - addTimeToExposure
  - addDaysExposed
  - addDaysPrescribed
  - addInitialExposureDuration
  - addInitialQuantity
  - addCumulativeQuantity
  - addInitialDailyDose
  - addCumulativeDose
- subtitle: Summarise treatment persistence using proportion of patients covered (PPC)
  desc: Summarise the proportion of patients in the drug cohort over time.
- contents:
  - summariseProportionOfPatientsCovered
  - tableProportionOfPatientsCovered
  - plotProportionOfPatientsCovered
- subtitle: Summarise treatments during certain windows
  desc: Summarise the use of different treatments during certain windows
- contents:
  - addTreatment
  - summariseTreatment
  - tableTreatment
  - plotTreatment
- subtitle: Summarise treatment restart or switch during certain time
  desc: Summarise the restart of a treatment, or switch to another, during certain time
- contents:
  - addDrugRestart
  - summariseDrugRestart
  - tableDrugRestart
  - plotDrugRestart
- subtitle: Daily dose documentation
  desc: Functions to assess coverage for the diferent ingredients and document how daily dose is calculated
- contents:
  - patternsWithFormula
  - patternTable
  - summariseDoseCoverage
  - tableDoseCoverage
- subtitle: Complementary functions
  desc: Complementary functions
- contents:
  - benchmarkDrugUtilisation
  - mockDrugUtilisation
- subtitle: Deprecated functions
  desc: This functions has been deprecated
- contents:
  - addExposedTime
  - addDailyDose
  - addRoute
  - addDrugUse
  - summariseDrugUse
  - dailyDoseCoverage
  - stratifyByUnit
  - readConceptList