data-raw/HK_delay_data.R

In covid-19-Re/estimateR: Reproductive number estimation from delayed observations of infections

## code to prepare `HK_delay_data` dataset goes here

max_delay_confirm <- 30
max_date <- as.Date("2020-08-01")

HK_linelist_data_url <- "https://api.data.gov.hk/v2/filter?q=%7B%22resource%22%3A%22http%3A%2F%2Fwww.chp.gov.hk%2Ffiles%2Fmisc%2Fenhanced_sur_covid_19_eng.csv%22%2C%22section%22%3A1%2C%22format%22%3A%22csv%22%7D"
HK_linelist_data <- try(readr::read_csv(HK_linelist_data_url,
  col_types = list(
    `Case no.` = readr::col_double(),
    `Report date` = readr::col_character(),
    `Date of onset` = readr::col_character(),
    Gender = readr::col_character(),
    Age = readr::col_double(),
    `Name of hospital admitted` = readr::col_character(),
    `Hospitalised/Discharged/Deceased` = readr::col_character(),
    `HK/Non-HK resident` = readr::col_character(),
    `Case classification*` = readr::col_character(),
    `Confirmed/probable` = readr::col_character()
  )
))

if ("try-error" %in% class(HK_linelist_data)) {
  stop(stringr::str_c("Couldn't read Hong Kong linelist data at ", HK_linelist_data_url))
}

HK_delay_data <- HK_linelist_data %>%
  dplyr::filter(.data$`Confirmed/probable` == "Confirmed") %>%
  # only keep confirmed cases
  dplyr::transmute(
    event_date = as.Date(.data$`Date of onset`, format = "%d/%m/%Y"), # rename/reformat columns
    report_date = as.Date(.data$`Report date`, format = "%d/%m/%Y")
  ) %>%
  dplyr::filter(!is.na(.data$event_date), !is.na(.data$report_date)) %>%
  dplyr::filter(.data$event_date < max_date) %>%
  dplyr::mutate(report_delay = as.integer(.data$report_date - .data$event_date)) %>%
  # extract reporting delays
  dplyr::mutate(report_delay = if_else(!between(.data$report_delay, 0, max_delay_confirm), # curate negative or too large reporting delays
    as.integer(NA),
    .data$report_delay
  )) %>%
  dplyr::filter(!is.na(.data$report_delay)) %>%
  # remove NA values
  dplyr::select(-.data$report_date) %>%
  # rearrange dataset
  dplyr::arrange(.data$event_date)

usethis::use_data(HK_delay_data, overwrite = TRUE, compress = "xz", version = 2)