## ----base, include = FALSE----------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  warning = FALSE, 
  message = FALSE,
  comment = "#>",
  fig.width = 7,
  fig.height = 5
)

## ----cdm----------------------------------------------------------------------
library(EpiStandard)
library(IncidencePrevalence)
library(omopgenerics)
library(dplyr)

cdm <- mockIncidencePrevalence(
  sampleSize = 10000,
  outPre = 0.25
)

## ----crude inc----------------------------------------------------------------
cdm <- generateDenominatorCohortSet(
  cdm = cdm,
  name = "denominator",
  cohortDateRange = as.Date(c("2008-01-01", "2020-01-01")),
  ageGroup = list(c(0, 19), c(20, 64), c(65, 150), c(0, 150)),
  sex = c("Male", "Female"),
  daysPriorObservation = 0
)

inc <- estimateIncidence(
  cdm = cdm,
  denominatorTable = "denominator",
  outcomeTable = "outcome",
  interval = c("years", "overall"),
  outcomeWashout = 0,
  repeatedEvents = FALSE
)

inc |> glimpse()

## ----tidy inc-----------------------------------------------------------------
incidenceTidy <- inc |>
  filterSettings(denominator_age_group %in% c("0 to 19", "20 to 64", "65 to 150")) |>
  asIncidenceResult()

incidenceTidy |> glimpse()

## ----standard pop-------------------------------------------------------------
standardPop <- mergeAgeGroups(
  standardPopulation("Europe"),
  newGroups = c("0 to 19", "20 to 64", "65 to 150")
) |>
  rename("denominator_age_group" = "age_group")
standardPop |> glimpse()

## ----standard inc-------------------------------------------------------------
standardInc <- directlyStandardiseRates(
  data = incidenceTidy,
  refdata = standardPop,
  event = "outcome_count",
  denominator = "person_years",
  age = "denominator_age_group",
  pop = "pop",
  strata = c("incidence_start_date", "denominator_sex", "analysis_interval", "outcome_cohort_name")
)
standardInc |> glimpse()