nhs_pathways_covid19: Potential COVID19 cases reported through NHS pathways
In reconhub/epichange: Detect Changes in Temporal Trends

Description Usage Format Author(s) Source Examples

This dataset contains daily numbers of reports on potential COVID-19 cases reported in England through the NHS pathways. This data is used for illustrative purpose, and was last updated on 1st June 2020. See example for a command line allowing to download the latest version.

1	nhs_pathways_covid19

A data.frame containing:

site_type: the system through which data were reported: 111/999 calls, or 111-online
date: the data of reporting
sex: the gender of the patient
age: the age of the patient, in years
ccg_code: NHS code for the Clinical Commissioning Groups (CCGs) (finer geographic unit)
ccg_name: name of the Clinical Commissioning Groups (CCGs) (smaller spatial unit)
count: number of potential COVID-19 cases reported
postcode: the postcode of the CCG
nhs_region: the NHS region (larger geographic unit)
day: the date as the number of days since the first reporting day
weekday: the day of the week, broken down into: weekend, Monday, and the rest of the week; this is used for modelling reporting effects

National Health Services (NHS) for England. Additional data and cleaning by Quentin Leclerc.

Data is available at https://digital.nhs.uk/dashboards/nhs-pathways; this precise dataset adds some cleaning and additional informaion (on NHS regions) and is taken from Quentin Leclerc's github repository: https://github.com/qleclerc/nhs_pathways_report

## Not run: 
# These commands will download the latest version of the data:
library(tidyverse)

# download data
pathways <- tempfile()
url <- paste0("https://github.com/qleclerc/nhs_pathways_report/",
              "raw/master/data/rds/pathways_latest.rds")
download.file(url, pathways)
pathways <- readRDS(pathways)


# add variables and subsets
day_of_week <- function(date) {
  day_of_week <- weekdays(date)
  out <- dplyr::case_when(
    day_of_week %in% c("Saturday", "Sunday") ~ "weekend",
    day_of_week %in% c("Monday") ~ "monday",
    TRUE ~ "rest_of_week"
  )
  out <- factor(out, levels = c("rest_of_week", "monday", "weekend"))
  out
}

pathways <- as_tibble(pathways) %>%
  mutate(nhs_region = stringr::str_to_title(gsub("_", " ", nhs_region)),
         nhs_region = gsub(" Of ", " of ", nhs_region),
         nhs_region = gsub(" And ", " and ", nhs_region),
         day = as.integer(date - min(date, na.rm = TRUE)),
         weekday = day_of_week(date))

## End(Not run)