Merge pull request #36 from humaniverse/health-index-ics

Health index ics

DESCRIPTION

@@ -11,7 +11,7 @@ Description: A package to distribute and summarise on UK health data.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Imports:
     tibble
 Depends: 

R/data.R

@@ -195,7 +195,7 @@ NULL
 
 #' England Health Index (ONS) - subdomains
 #'
-#' A dataset containing overall health index scores for the English lower tier
+#' A dataset containing subdomain health index scores for the English lower tier
 #' local authorities from 2015-2021.
 #'
 #' @format A data frame with 2,149 rows and 16 variables:
@@ -237,6 +237,59 @@ NULL
 #' @source \url{https://www.ons.gov.uk/}
 "england_health_index_indicators"
 
+#' England Health Index (ONS)
+#'
+#' A dataset containing overall health index scores for the English Integrated
+#' Care Boards from 2015-2021.
+#'
+#' @format A data frame with 294 rows and 7 variables:
+#' \describe{
+#'   \item{icb22_code}{2022 Integrated Care Board code}
+#'   \item{icb22_name}{2022 Integrated Care Board name}
+#'   \item{year}{Year}
+#'   \item{overall_score}{The overall health index score}
+#'   \item{healthy_people_domain_score}{Score for the Healthy People domain}
+#'   \item{healthy_lives_domain_score}{Score for the Healthy Lives domain}
+#'   \item{healthy_places_domain_score}{Score for the Healthy Places domain}
+#'   ...
+#' }
+#' @source \url{https://www.ons.gov.uk/}
+"england_health_index_ics"
+
+#' England Health Index (ONS) - subdomains
+#'
+#' A dataset containing subdomain health index scores for the English Integrated
+#' Care Boards from 2015-2021.
+#'
+#' @format A data frame with 4,116 rows and 5 variables:
+#' \describe{
+#'   \item{icb22_code}{2022 Integrated Care Board code}
+#'   \item{icb22_name}{2022 Integrated Care Board name}
+#'   \item{year}{Year}
+#'   \item{sub_domain}{The name of the subdomain}
+#'   \item{value}{The value of the indicator}
+#'   ...
+#' }
+#' @source \url{https://www.ons.gov.uk/}
+"england_health_index_ics_indicators"
+
+#' England Health Index (ONS) - underlying indicators
+#'
+#' A dataset containing underlying indicators for the ONS Health Index for
+#' English Integrated Care Boards from 2015-2021.
+#'
+#' @format A data frame with 16,464 rows and 5 variables:
+#' \describe{
+#'   \item{icb22_code}{2022 Integrated Care Board code}
+#'   \item{icb22_name}{2022 Integrated Care Board name}
+#'   \item{year}{Year}
+#'   \item{indicator}{The name of the indicator}
+#'   \item{value}{The value of the indicator}
+#'   ...
+#' }
+#' @source \url{https://www.ons.gov.uk/}
+"england_health_index_ics_indicators"
+
 #' Legal Partnership Status, England, 2021
 #'
 #' A dataset containing legal partnership status data at LTLA level

data-raw/england-health-index-ics.R

@@ -0,0 +1,92 @@
+# ---- Load libs ----
+library(tidyverse)
+library(readxl)
+library(httr2)
+
+# ---- Load internal sysdata.rda file with URL's ----
+pkgload::load_all(".")
+
+# ---- Download data ----
+query_url <-
+  query_urls |>
+  filter(id == "england_health_index_ics") |>
+  pull(query)
+
+download <- tempfile(fileext = ".xlsx")
+
+request(query_url) |>
+  req_perform(download)
+
+# ---- Read sheets ----
+overall_scores_raw <- read_excel(
+  download,
+  sheet = "Table_2_Index_scores",
+  range = "A3:I45"
+)
+
+sheet_names <- paste0("Table_", seq(3, 9), "_", seq(2021, 2015), "_Index")
+index_names <- paste0("index_", seq(2021, 2015))
+
+indices <- map(
+  .x = set_names(sheet_names, index_names),
+  .f = \(x) read_excel(download, sheet = x, range = "A5:BW47")
+)
+
+# ---- Clean data ----
+overall_scores <- overall_scores_raw |>
+  rename(icb22_code = `Area Code`, icb22_name = `Area Name`) |>
+  pivot_longer(
+    cols = `2015`:`2021`, names_to = "year", values_to = "overall_score"
+  ) |>
+  mutate(year = as.integer(year))
+
+domain_scores <- map2(
+  .x = indices,
+  .y = seq(2021, 2015),
+  .f = \(x, y) {
+    x |>
+      rename(icb22_code = `Area Code`, icb22_name = `Area Name`) |>
+      select(starts_with("icb22_"), ends_with("Domain")) |>
+      janitor::clean_names() |>
+      mutate(year = y)
+  }
+) |>
+  list_rbind()
+
+england_health_index_ics <- left_join(overall_scores, domain_scores)
+
+england_health_index_ics_subdomains <- map2(
+  .x = indices,
+  .y = seq(2021, 2015),
+  .f = \(x, y) {
+    x |>
+      rename(icb22_code = `Area Code`, icb22_name = `Area Name`) |>
+      select(starts_with("icb22_"), matches("\\[(Pe|Pl|L)\\]$")) |>
+      rename_with(~ str_remove(., " \\[.*\\]$")) |>
+      janitor::clean_names() |>
+      pivot_longer(cols = !starts_with("icb22_"), names_to = "sub_domain") |>
+      mutate(year = y) |>
+      relocate(year, .after = "icb22_name")
+  }
+) |>
+  list_rbind()
+
+england_health_index_ics_indicators <- map2(
+  .x = indices,
+  .y = seq(2021, 2015),
+  .f = \(x, y) {
+    x |>
+      rename(icb22_code = `Area Code`, icb22_name = `Area Name`) |>
+      select(!c(matches("\\[(Pe|Pl|L)\\]$"), matches("Domain$"))) |>
+      rename_with(~ str_remove(., " \\[.*\\]$")) |>
+      janitor::clean_names() |>
+      pivot_longer(cols = !starts_with("icb22_"), names_to = "indicator") |>
+      mutate(year = y) |>
+      relocate(year, .after = "icb22_name")
+  }
+) |>
+  list_rbind()
+
+usethis::use_data(england_health_index_ics, overwrite = TRUE)
+usethis::use_data(england_health_index_ics_subdomains, overwrite = TRUE)
+usethis::use_data(england_health_index_ics_indicators, overwrite = TRUE)

data-raw/query-urls.R

@@ -70,6 +70,7 @@ query_urls <-
     "Disability", "england_disability_2021", "2021", "OGLv3", "https://www.nomisweb.co.uk/output/census/2021/census2021-ts038.zip", "https://www.nomisweb.co.uk/sources/census_2021_bulk",
     "Health Index", "england_health_index_2021", "June 2021", "OGLv3", "https://www.ons.gov.uk/file?uri=/peoplepopulationandcommunity/healthandsocialcare/healthandwellbeing/datasets/healthindexscoresengland/current/healthindexscoresengland.xlsx", "https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/healthandwellbeing/datasets/healthindexscoresengland",
     "Health Index underlying indicators", "england_health_index_2021_indicators", "June 2021", "OGLv3", "https://www.ons.gov.uk/file?uri=/peoplepopulationandcommunity/healthandsocialcare/healthandwellbeing/datasets/healthindexunderlyingdataengland/current/healthindexunderlyingdataenglandcanscreenfix.xlsx", "https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/healthandwellbeing/datasets/healthindexunderlyingdataengland",
+    "Health Index ICS", "england_health_index_ics", "2015-2021", "OGLv3", "https://www.ons.gov.uk/file?uri=/peoplepopulationandcommunity/healthandsocialcare/healthandwellbeing/datasets/healthindexscoresintegratedcaresystemsengland/current/healthindexscoresintegratedcaresystemsenglandcanscreeningfix.xlsx", "https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/healthandwellbeing/datasets/healthindexscoresintegratedcaresystemsengland",
     "Homelessness", "england_homelessness", "October to December 2023", "", "https://assets.publishing.service.gov.uk/media/662f6eccce557c60ed19ad15/Detailed_LA_202312.ods", "https://www.gov.uk/government/statistical-data-sets/live-tables-on-homelessness",
     "Hospital discharge (criteria to reside)", "nhs_hospital_discharge_data_april_22", "April 2022", "OGLv3", "https://www.england.nhs.uk/statistics/wp-content/uploads/sites/2/2022/08/Daily-discharge-sitrep-monthly-data-webfile-April2022-v2.xlsx", "https://www.england.nhs.uk/statistics/statistical-work-areas/discharge-delays-acute-data/",
     "Hospital discharge (criteria to reside)", "nhs_hospital_discharge_data_may_22", "May 2022", "OGLv3", "https://www.england.nhs.uk/statistics/wp-content/uploads/sites/2/2022/08/Daily-discharge-sitrep-monthly-data-webfile-May2022-v2.xlsx", "https://www.england.nhs.uk/statistics/statistical-work-areas/discharge-delays-acute-data/",