Add validation data for consultations

lib/functions/function_get_validation_data.R

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+library(httr)
+library(here)
+library(rvest)
+library(dplyr)
+library(lubridate)
+library(tidyverse)
+library(readr)
+
+#' Extract dates from dispensing data URL
+#'
+#' @param urls List of URLs
+#' @return String, of date in YYYY-MM-DD format if date can be found, otherwise NA.
+extract_dates <- function(urls) {
+  urls %>%
+    map(~ {
+      match <- str_match(.x, ".*Dispensing%20Data%20(\\w+)%20(\\d{2})")[, 2:3]
+
+      if (all(!is.na(match))) {
+        month <- match[1]
+        year <- paste0("20", match[2])
+
+        parsed_date <- parse_date_time(
+          paste("1", month, year),
+          orders = "dmy",
+          quiet = TRUE
+        )
+        if (!is.na(parsed_date)) {
+          return(format(parsed_date, "%Y-%m-%d"))
+        }
+      }
+      return(NA)
+    })
+}
+
+get_dispensing_urls <- function(start_date = NULL, end_date = NULL) {
+  # This is the URL where the data is linked from
+  url <- "https://www.nhsbsa.nhs.uk/prescription-data/dispensing-data/dispensing-contractors-data"
+
+  # The URL to the data we are interested in follows this URL structure
+  # https://www.nhsbsa.nhs.uk/sites/default/files/2024-05/Dispensing%20Data%20Jan%2024%20-%20CSV.csv
+  base_url <- "https://www.nhsbsa.nhs.uk"
+
+  response <- GET(url)
+  html_content <- content(response, "text", encoding = "UTF-8")
+
+  csv_links <- read_html(html_content) %>%
+    html_nodes("a") %>%
+    html_attr("href") %>%
+    .[grepl("Dispensing%20Data.*\\.csv", .)]
+
+  df <- tibble(
+    date = as.Date(extract_dates(csv_links) |> unlist()),
+    url = paste0(base_url, csv_links)
+  )
+
+  if (is.null(start_date)) {
+    start_date <- as.Date(min(df$date))
+  }
+
+  if (is.null(end_date)) {
+    end_date <- as.Date(max(df$date))
+  }
+
+  df <- df |>
+    filter(between(date, as.Date(start_date), as.Date(end_date)))
+
+  setNames(as.list(df$url), as.character(df$date))
+}
+
+get_dispensing_data <- function(start_date = NULL, end_date = NULL) {
+  dispensing_urls <- get_dispensing_urls(start_date = start_date, end_date = end_date)
+
+  icb_var_list <- c(
+    "ICBCode",
+    "ICB"
+  )
+
+  pf_var_list <- c(
+    "NumberofPharmacyFirstClinicalPathwaysConsultations-AcuteOtitisMedia",
+    "NumberofPharmacyFirstClinicalPathwaysConsultations-AcuteSoreThroat",
+    "NumberofPharmacyFirstClinicalPathwaysConsultations-Impetigo",
+    "NumberofPharmacyFirstClinicalPathwaysConsultations-InfectedInsectBites",
+    "NumberofPharmacyFirstClinicalPathwaysConsultations-Shingles",
+    "NumberofPharmacyFirstClinicalPathwaysConsultations-Sinusitis",
+    "NumberofPharmacyFirstClinicalPathwaysConsultations-UncomplicatedUTI",
+    "NumberofPharmacyFirstUrgentMedicineSupplyConsultations",
+    "NumberofPharmacyFirstMinorIllnessReferralConsultations"
+  )
+
+  df <- dispensing_urls |>
+    map(read_csv,
+      name_repair = janitor::make_clean_names
+    ) |>
+    bind_rows(.id = "date") |>
+    select(date, all_of(janitor::make_clean_names(c(icb_var_list, pf_var_list))))
+
+  df |>
+    rename_with(~ str_replace(., "^numberof_pharmacy_first", "n_pf")) |>
+    rename_with(~ str_replace(., "clinical_pathways_consultations", "consultation"))
+}
+
+# Calculate summary of counts
+df_dispensing_data <- get_dispensing_data(start_date = "2024-02-01")
+
+df_dispensing_data_summary <- df_dispensing_data |>
+  group_by(date) |>
+  summarise(
+    n_pf_consultation_acute_otitis_media = sum(n_pf_consultation_acute_otitis_media, na.rm = TRUE),
+    n_pf_consultation_acute_sore_throat = sum(n_pf_consultation_acute_sore_throat, na.rm = TRUE),
+    n_pf_consultation_impetigo = sum(n_pf_consultation_impetigo, na.rm = TRUE),
+    n_pf_consultation_infected_insect_bites = sum(n_pf_consultation_infected_insect_bites, na.rm = TRUE),
+    n_pf_consultation_shingles = sum(n_pf_consultation_shingles, na.rm = TRUE),
+    n_pf_consultation_sinusitis = sum(n_pf_consultation_sinusitis, na.rm = TRUE),
+    n_pf_consultation_uncomplicated_uti = sum(n_pf_consultation_uncomplicated_uti, na.rm = TRUE),
+    # n_pf_urgent_medicine_supply_consultations = sum(n_pf_urgent_medicine_supply_consultations, na.rm = TRUE),
+    # n_pf_minor_illness_referral_consultations = sum(n_pf_minor_illness_referral_consultations, na.rm = TRUE)
+  ) |>
+  pivot_longer(cols = c(
+    n_pf_consultation_acute_otitis_media,
+    n_pf_consultation_acute_sore_throat,
+    n_pf_consultation_impetigo,
+    n_pf_consultation_infected_insect_bites,
+    n_pf_consultation_shingles,
+    n_pf_consultation_sinusitis,
+    n_pf_consultation_uncomplicated_uti,
+    # n_pf_urgent_medicine_supply_consultations,
+    # n_pf_minor_illness_referral_consultations
+  ),
+  names_to = "consultation_type",
+  values_to = "count") |>
+  mutate(consultation_type = str_replace(consultation_type, "^n_pf_consultation_", ""))
+
+write_csv(df_dispensing_data_summary, here("lib", "validation", "data", "pf_consultation_validation_data.csv"))

lib/validation/data/pf_consultation_validation_data.csv

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+date,consultation_type,count
+2024-02-01,acute_otitis_media,18893
+2024-02-01,acute_sore_throat,41014
+2024-02-01,impetigo,6816
+2024-02-01,infected_insect_bites,3412
+2024-02-01,shingles,4078
+2024-02-01,sinusitis,18384
+2024-02-01,uncomplicated_uti,32678
+2024-03-01,acute_otitis_media,22888
+2024-03-01,acute_sore_throat,54756
+2024-03-01,impetigo,6740
+2024-03-01,infected_insect_bites,4180
+2024-03-01,shingles,4069
+2024-03-01,sinusitis,17220
+2024-03-01,uncomplicated_uti,34536
+2024-04-01,acute_otitis_media,19295
+2024-04-01,acute_sore_throat,56925
+2024-04-01,impetigo,7191
+2024-04-01,infected_insect_bites,6099
+2024-04-01,shingles,4470
+2024-04-01,sinusitis,17715
+2024-04-01,uncomplicated_uti,41951
+2024-05-01,acute_otitis_media,20240
+2024-05-01,acute_sore_throat,58022
+2024-05-01,impetigo,6235
+2024-05-01,infected_insect_bites,19010
+2024-05-01,shingles,4691
+2024-05-01,sinusitis,15909
+2024-05-01,uncomplicated_uti,44340
+2024-06-01,acute_otitis_media,15826
+2024-06-01,acute_sore_throat,52288
+2024-06-01,impetigo,6362
+2024-06-01,infected_insect_bites,27294
+2024-06-01,shingles,4626
+2024-06-01,sinusitis,15052
+2024-06-01,uncomplicated_uti,43289
+2024-07-01,acute_otitis_media,17682
+2024-07-01,acute_sore_throat,54859
+2024-07-01,impetigo,6740
+2024-07-01,infected_insect_bites,36370
+2024-07-01,shingles,5103
+2024-07-01,sinusitis,14115
+2024-07-01,uncomplicated_uti,51321