R/get_linelist.r

In epiforecasts/WuhanSeedingVsTransmission: The transmissibility of novel Coronavirus in the early stages of the 2019-20 outbreak in Wuhan

##' Get the latest compiled linelist
##'
##' @return a tibble with the linelist
##'   delays to randomly sample
##' @importFrom readr read_csv
##' @importFrom dplyr bind_rows rename mutate mutate_at
##' @importFrom purrr map
##' @importFrom stringr str_trim
##' @author Sebastian Funk <sebastian.funk@lshtm.ac.uk>
##'
##' @export
##' 
##' @examples 
##' 
##' ## Example
##' \dontrun{
##' get_linelist()
##' }
##' 
##' ## Code
##' get_linelist
get_linelist <- function() {
  
  ## CRAN check - dealing with global variables
  date_onset_symptoms_str <- NULL; date_admission_hospital_str <- NULL;
  ate_confirmation_str <- NULL; date_confirmation <- NULL;
  date_onset_symptoms <- NULL; date_onset_symptoms <- NULL;
  date_admission_hospital <- NULL; date_confirmation_str <- NULL;
  
  
  
  gids <- c(outside_hubei = 0, hubei = 429276722)
  urls <- paste0("https://docs.google.com/spreadsheets/d/",
           "1itaohdPiAeniCXNlntNztZ_oRvjh0HsGuJXUJWET008/pub",
           "?single=true&output=csv&gid=", gids)
  linelists <- lapply(urls, readr::read_csv)
  
  ## Drop columns
  drops <- c("chroDisea_Yes(1)/No(0)")
  linelists[[1]] <- linelists[[1]][ , !(names(linelists[[1]]) %in% drops)]
  linelists[[2]] <-  linelists[[2]][ , !(names(linelists[[2]]) %in% drops)]
  
  ##Munge dataset specific data
  linelists <- linelists %>% 
    purrr::map(
      function(data) {
        dplyr::mutate_at(data,
                         .vars = c("longitude", "latitude"), 
                         ~ ifelse(. %in% "#REF!", NA, .) %>% 
                           stringr::str_trim() %>% 
                           as.numeric())
        })
  
  linelists <- dplyr::bind_rows(linelists) %>% 
    dplyr::rename(
      date_onset_symptoms_str = "date_onset_symptoms",
      date_admission_hospital_str = "date_admission_hospital",
      date_confirmation_str = "date_confirmation"
    ) %>%
    dplyr::mutate(
      date_onset_symptoms =
        as.Date(date_onset_symptoms_str, format = "%d.%m.%Y"),
      date_admission_hospital =
        as.Date(date_admission_hospital_str, format = "%d.%m.%Y"),
      date_confirmation =
        as.Date(date_confirmation_str, format = "%d.%m.%Y")
    ) %>%
    dplyr::mutate(
      delay_confirmation =
        date_confirmation - date_onset_symptoms,
      delay_admission =
        date_admission_hospital - date_onset_symptoms
    )
  
  return(linelists)
}