R/haiti2_data.R

In zjiang2/haitipkg: R Package for Haiti Article

#' Clean haiti cases data for Model 2
#'
#' Generate a data frame of department level reported cases of cholera
#' in Haiti.
#'
#' @param recreate a boolean indicating whether or not we want to recreate the results from lee20.
#'
#' @return Data frame
#' @examples
#' haiti2_data()
#' @export

haiti2_data <- function(recreate = TRUE){

  if (recreate) {
    path <- system.file("extdata", "haiti-data-from-2010-10-to-2019-01.csv", package = 'haitipkg')
    haiti <- utils::read.csv(path)
  } else {
    haiti <- haitiCholera
  }

  haiti <- haiti |> dplyr::select(-report)

  dates <- c("2017-04-22","2018-01-27","2018-09-22","2018-12-01")
  r <- rbind(rep(NA,10),rep(NA,10),rep(NA,10),rep(NA,10))

  final <- cbind(dates,r) |> as.data.frame()
  colnames(final) <- colnames(haiti)

  final <- rbind(haiti, final)
  final <- dplyr::arrange(final, date_saturday)

  haiti <- reshape2::melt(final, id.vars="date_saturday")
  colnames(haiti) <- c("year","department","cases")
  haiti$year <- lubridate::decimal_date(lubridate::ymd(haiti$year))
  haiti$department <- as.character(haiti$department)
  haiti$cases <- as.numeric(haiti$cases)

  return(haiti)
}