R/read_entry.R

In jarad/FluSight: Utility functions for the CDC FluSight competition

#' Read in a csv entry file
#'
#' This function reads in the csv file and arranges it for consistency.
#'
#' @param file A csv file path
#' @return An arranged data.frame
#' @import dplyr
#' @export
read_entry = function(file) {

  entry <- read.csv(file,
                    colClasses = "character",      # Due to bin_start_incl "none"
                    stringsAsFactors = FALSE)

  names(entry) <- tolower(names(entry))
  
  
  entry <- entry %>%
            mutate(value = as.numeric(value),
                   bin_start_incl = trimws(replace(bin_start_incl,
                                            !is.na(bin_start_incl) & bin_start_incl != "none",
                                            format(round(as.numeric(
                                              bin_start_incl[!is.na(bin_start_incl) & bin_start_incl != "none"])
                                              , 1), nsmall = 1))),
                   bin_end_notincl = trimws(replace(bin_end_notincl,
                                            !is.na(bin_end_notincl) & bin_end_notincl != "none",
                                            format(round(as.numeric(
                                              bin_end_notincl[!is.na(bin_end_notincl) & bin_end_notincl != "none"])
                                              , 1), nsmall = 1))))

  # Add forecast week to imported data
  forecast_week <- as.numeric(gsub("EW", "", 
                                   regmatches(file, regexpr("(?:EW)[0-9]{2}", file))))
  
  
  if (length(forecast_week > 0))
     entry <- dplyr::mutate(entry, forecast_week  = forecast_week)


  FluSight::arrange_entry(entry = entry)
}

#' Arrange an entry for consistency
#'
#' @param entry A data.frame
#' @return An arranged data.frame
#' @import dplyr
#' @export
#' @keywords internal
arrange_entry <- function(entry) {

  FluSight::verify_colnames(entry, check_week = F)

  # Arrange entry by type, location, target, bin
  entry %>%
    dplyr::arrange(type, location, target) %>% 
    dplyr::select(location, target, type, unit, bin_start_incl,
                  bin_end_notincl, value, everything())

}