R/ds_gov.tw.R

In covid19datahub/COVID19dev: COVID-19 Data Hub

#' Ministry of Health and Welfare of Taiwan
#'
#' Data source for: Taiwan
#'
#' @param level 1, 2
#'
#' @section Level 1:
#' - confirmed cases
#' - tests
#'
#' @section Level 2:
#' - confirmed cases
#'
#' @source https://data.gov.tw
#'
#' @keywords internal
#'
gov.tw <- function(level) {
  if(!level %in% 1:2) return(NULL)

  # download cases
  url <- "https://od.cdc.gov.tw/eic/Day_Confirmation_Age_County_Gender_19CoV.csv"
  x   <- read.csv(url, encoding = "UTF-8")
  
  # format cases
  x <- x[,-1]
  colnames(x) <- c("date", "county", "city", "gender", "imported", "age_group", "confirmed")
  
  # convert date
  x$date <- as.Date(x$date, "%Y/%m/%d")

  if(level == 1) {
    
    # download tests
    # see https://data.gov.tw/dataset/120451
    url.tests <- "https://od.cdc.gov.tw/eic/covid19/covid19_tw_specimen.csv"
    x.tests   <- read.csv(url.tests, encoding = "UTF-8")
    
    # format tests
    colnames(x.tests) <- c("date", "notification", "home quarantine", "monitoring", "total")
    x.tests <- x.tests %>%
      # convert date
      mutate(date  = as.Date(date, "%Y/%m/%d")) %>%
      # sort by date
      arrange(date) %>%
      # cumulate
      mutate(tests = cumsum(total)) %>%
      # subset
      select(date, tests) %>%
      # drop missing values
      filter(!is.na(tests))
    
    # cases
    x <- x %>% 
      # for each date
      group_by(date) %>%
      # compute total counts
      summarise(confirmed = sum(confirmed)) %>%
      # sort by date
      arrange(date) %>%
      # cumulate
      mutate(confirmed = cumsum(confirmed))
      
    # merge
    x <- full_join(x, x.tests, by = "date")
    
  }
  
  if(level == 2) {
    
    # drop unassigned
    x <- filter(x, x$county!="空值")

    # cases
    x <- x %>% 
      # for each date and countr
      group_by(date, county) %>%
      # compute total counts
      summarise(confirmed = sum(confirmed)) %>%
      # group by county
      group_by(county) %>%
      # sort by date
      arrange(date) %>%
      # cumulate
      mutate(confirmed = cumsum(confirmed))
    
  }
    
  # fix date
  x <- x[x$date<=Sys.Date(),]
  
  return(x)
}