Merge pull request #31 from humaniverse/cancer-screening

First draft completed - cancer-screening

R/data.R

@@ -1,3 +1,22 @@
+#' Percentage of Cancer Screening Uptake (2022-2023)
+#'
+#' A dataset containing statistics on the percentage of cancer screening uptake
+#' in each Northern Irish Council, 2022-2023.
+#'
+#'
+#' @format A data frame with 11 rows and 3 variables:
+#' \describe{
+#' \item{ltla24_code}{Local Authority Code}
+#' \item{cancer_screening_uptake}{Percentage of cancer screening uptake; breast,
+#' bowel, and cervical cancer.}
+#' \item{year}{Time period}
+#'
+#' ...
+#' }
+#' @source \url{https://www.publichealth.hscni.net/publications/director-public-health-core-tables-2022}
+#'
+"lives_cancer_screening"
+
 #' Percentage of Absolute Child Poverty (2017)
 #'
 #' A dataset containing statistics on the percentage of children (aged 15 and

data-raw/healthy-lives/cancer-screening.R

@@ -0,0 +1,89 @@
+# ---- Load packages ----
+library(tidyverse)
+library(httr)
+library(readxl)
+library(geographr)
+
+# ---- Get and clean data ----
+# Geographical Code Data: Health Board and Local Authority
+
+hb_ltla_lookup <- lookup_ltla21_hsct18 |>
+  distinct(ltla21_code, trust18_code)
+
+hb_lookup <- boundaries_trusts_ni18 |>
+  sf::st_drop_geometry()
+
+# Cancer Screening data
+# Source: https://www.publichealth.hscni.net/publications/director-public-health-core-tables-2022
+
+GET(
+  "https://www.publichealth.hscni.net/sites/default/files/2024-04/Core%20Tables%202022%20-%20Excel%20tables_1.xlsx",
+  write_disk(tf <- tempfile(fileext = ".xlsx"))
+)
+
+
+# Cervical Cancer
+cervical_raw <- read_excel(tf, sheet = 34, skip = 3)
+
+cervical_hb <- cervical_raw |>
+  slice(1:5) |>
+  select(
+    trust18_name = HSCT,
+    cervical_screening_percentage = `% Coverage`
+  )
+
+
+# Breast Cancer
+breast_raw <- read_excel(tf, sheet = 35, skip = 3)
+
+breast_hb <- breast_raw |>
+  slice(1:5) |>
+  select(
+    trust18_name = `HSC Trust of residence`,
+    breast_screening_percentage = `%`
+  )
+
+
+# Bowel Cancer
+bowel_raw <- read_excel(tf, sheet = 37, skip = 3)
+
+bowel_hb <- bowel_raw |>
+  slice(1:5) |>
+  select(
+    trust18_name = `HSCT`,
+    bowel_screening_percentage = `Uptake for bowel cancer screening \r\n(%)`
+  )
+
+# Join datasets
+# Cancer Screening Percentages
+
+cancer_screening_hb <- cervical_hb |>
+  left_join(breast_hb) |>
+  left_join(bowel_hb) |>
+  rowwise() |>
+  mutate(
+    total_cancer_screening_percentage = mean(c_across(c(cervical_screening_percentage, breast_screening_percentage, bowel_screening_percentage)), na.rm = TRUE)
+  ) |>
+  ungroup()
+
+# Cancer screening data + Trust name and code
+cancer_screening_hb <- cancer_screening_hb |>
+  left_join(hb_lookup) |>
+  select(
+    -trust18_name, -cervical_screening_percentage, -breast_screening_percentage, -bowel_screening_percentage
+    ) |>
+  relocate(trust18_code)
+
+# Cancer screening data + LA code
+lives_cancer_screening <- cancer_screening_hb |>
+  left_join(hb_ltla_lookup) |>
+  mutate(year = "2022-23") |>
+  select(
+    ltla24_code = ltla21_code,
+    cancer_screening_uptake = total_cancer_screening_percentage,
+    year
+  ) |>
+  arrange(ltla24_code)
+
+# ---- Save output to data/ folder ----
+usethis::use_data(lives_cancer_screening, overwrite = TRUE)

metadata.md

@@ -16,7 +16,7 @@
 | Healthy Lives |Cardiovascular Conditions | 2023/24 | [NISRA](https://data.nisra.gov.uk/k) | [OGL3](https://www.ninis2.nisra.gov.uk/public/terms.aspx) | :heavy_check_mark: Indicator: Percentage rate of people self-reported as having CHD, Atrial Fibrillation, Heart Failure, and/or Stroke & TIA. | :heavy_check_mark: |
 | Healthy Lives | High Blood Pressure | 2023-24 | [NISRA](https://data.nisra.gov.uk/) | [OGL3](https://www.ninis2.nisra.gov.uk/public/terms.aspx) | :heavy_check_mark: Indicator: Percentage of adults with high blood pressure | :heavy_check_mark: |
 | Healthy Lives | Overweight and Obesity in Adults | :x: | :x: | :x: | :x: - Data unavailable. | :x: |
-| Healthy Lives | Cancer Screening | 2023-24 | [NISRA](https://data.nisra.gov.uk/) | [OGL3](https://www.nisra.gov.uk/crown-copyright) | :heavy_check_mark: Indicator: Percentage of people with cancer| :heavy_check_mark: |
+| Healthy Lives | Cancer Screening | 2022/23 | [Public Health](https://www.publichealth.hscni.net/publications/director-public-health-core-tables-2022) | [OGL3](https://www.ninis2.nisra.gov.uk/public/terms.aspx)| heavy_check_mark: Indicator: Percentage of bowel, breast, and cervical cancer screening uptake. | :heavy_check_mark: |
 | Healthy Lives | Sexual Health | :x: | :x: | :x: | :x: - Data unavailable. | :x: |
 | Healthy Lives | Vaccination Coverage | 2022/23 | [Public Health](https://www.publichealth.hscni.net/publications/director-public-health-core-tables-2022) | [OGL3](https://www.ninis2.nisra.gov.uk/public/terms.aspx) | :heavy_check_mark: Indicator: Percentage of vaccine coverage in children 6 and under | :heavy_check_mark: |