R/readWHO.R

In pik-piam/mrcommons: MadRat commons Input Data Library

#' Read WHO
#'
#' Read-in WHO (World health organization) data files as magpie object.
#' The files contain information on physical inactivity
#'
#'
#' @param subtype Type of WHO data that should be read. Includes
#' physical_inactivity_adults and physical_inactivity_underaged
#' @return magpie object of the WHO data
#' @author Benjamin Bodirsky
#' @seealso [readSource()]
#' @examples
#' \dontrun{
#' a <- readSource(type = "WHO", subtype = "physical_activity_adults")
#' }
#'
readWHO <- function(subtype) {

  reformat <- function(x) {
    x <- strsplit(x, split = " ")
    x <- unlist(lapply(x, FUN = function(x) {
return(x[[1]])
}))
    x[x == "No"] <- NA
    x <- as.numeric(x)
    return(x)
  }

  if (subtype == "physical_inactivity_adults") {
    a <- read.csv("NCD_PAC,NCD_PAA.csv", stringsAsFactors = FALSE)
  } else if (subtype == "physical_inactivity_underaged") {
    a <- read.csv("NCD_PAC_ADO.csv", stringsAsFactors = FALSE)
  }

  a <- a[, c(1, 2, 5, 6)]
  a <- a[-1, ]
  colnames(a) <- c("iso", "year", "M", "F")

  a$M <- reformat(a$M)
  a$F <-  reformat(a$F)
  a$year <- sub(a$year, pattern = " ", replacement = "y")

  a$iso <- toolCountry2isocode(a$iso, mapping = c(
    "bolivia (plurinational state of)" = "BOL",
    "micronesia (federated states of)" = "FSM",
    "the former yugoslav republic of macedonia" = "MKD",
    "united kingdom of great britain and northern ireland" = "GBR",
    "venezuela (bolivarian republic of)" = "VEN"
  ))
  out <- as.magpie(a)

  return(out)
}