## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----example 1----------------------------------------------------------------
library(dplyr)
library(EpiStandard)

brain_cancer_2022 <- data.frame(
  age_group = c("0 to 4","5 to 9", "10 to 14", "15 to 19","20 to 24","25 to 29","30 to 34","35 to 39","40 to 44","45 to 49","50 to 54","55 to 59",
                "60 to 64", "65 to 69", "70 to 74", "75 to 79", "80 to 84", "85 to 89", "90 to 150"),
  cases = c(5,4,4,4,2,6,6,14,8,9,17,19,34,30,39,41,23,13,7),
  denominator = c(152519,174409,186628,177708,184964,187669,199578,192117,181871,176614,213390,224095,206338,180033,173220,144499,90861,54621,30506))

standard <- standardPopulation(region = "Europe")

## ----example 1.5--------------------------------------------------------------

directlyStandardiseRates(data = brain_cancer_2022,
                          event = "cases",
                          denominator = "denominator",
                          age = "age_group",
                          pop = "pop",
                          refdata = standard) |>
  glimpse()


## ----example 3----------------------------------------------------------------
wales_standard <- data.frame(
  age_group = c("0 to 4","5 to 9", "10 to 14", "15 to 19","20 to 24","25 to 29","30 to 34","35 to 39","40 to 44","45 to 49","50 to 54","55 to 59",
                "60 to 64", "65 to 69", "70 to 74", "75 to 79", "80 to 84", "85 to 89", "90 to 150"),
  pop = c(162528,165436,175568,182829,194959,186466,187941,188607,198164,207383,
          213638,209169,206018,176291,163639,129008,95844,63537,39003)
)

directlyStandardiseRates(data = brain_cancer_2022,
                          event = "cases",
                          denominator = "denominator",
                          age = "age_group",
                          pop = "pop",
                          refdata = wales_standard) |>
  glimpse()


## ----example 2----------------------------------------------------------------
brain_cancer_2122 <- data.frame(
  age_group = rep(c("0 to 4","5 to 9", "10 to 14", "15 to 19","20 to 24","25 to 29","30 to 34","35 to 39","40 to 44","45 to 49","50 to 54","55 to 59",
                "60 to 64", "65 to 69", "70 to 74", "75 to 79", "80 to 84", "85 to 89", "90 to 150"),2),
  cases = c(5,4,4,4,2,6,6,14,8,9,17,19,34,30,39,41,23,13,7,
            5,6,5,5,1,3,3,6,12,14,24,18,21,22,36,38,28,17,2),
  denominator = c(152519,174409,186628,177708,184964,187669,199578,192117,181871,176614,213390,224095,206338,180033,173220,144499,90861,54621,30506,
                  153564,175351,183177,174911,185152,185530,196157,186861,176206,183537,215783,222933,200666,178021,181109,133820,89018,53636,30201),
  year = c(rep("2022",19), rep("2021", 19))
)

directlyStandardiseRates(data = brain_cancer_2122,
                          event = "cases",
                          denominator = "denominator",
                          age = "age_group",
                          pop = "pop",
                          strata = "year",
                          refdata = wales_standard) |> 
  glimpse()