R/injury_death_to_yll.R

In danielgils/cobeneficioswwf: Evaluación de Cobeneficios WWF

#' Map injury death burden to YLL burden
#'
#' Calculated the YLL burden from the death burden of injury based on the ratio in the GBD data.
#'
#' @param injuries data frame of injury deaths
#'
#' @return list of injury deaths and YLLs (which are differences from reference scenario) plus the values in the reference scenario.
#'
#' @export
injury_death_to_yll <- function(injuries){
  # injuries is a tibble, GBD_INJ_YLL is a data.frame, returns a tibble
  joined_injury <- dplyr::left_join(injuries, GBD_INJ_YLL[,c('sex_age','sex','yll_dth_ratio')], by = c("sex_age",'sex'))
  # Estimate YLLs using predicted deaths and the average YLLs from gbd dataset
  joined_injury$YLL <- joined_injury$Deaths * joined_injury$yll_dth_ratio
  death_and_yll <- dplyr::select(joined_injury,
                                 c('age_cat','sex','scenario','Deaths','YLL'))

  x_deaths <- dplyr::select(death_and_yll, -YLL)
  x_deaths <- spread(x_deaths,scenario, Deaths)
  x_yll <- dplyr::select(death_and_yll, -Deaths)
  x_yll <- spread(x_yll,scenario, YLL)

  ref_scen <- REFERENCE_SCENARIO
  ref_scen_index <- which(SCEN == ref_scen)
  calc_scen <- SCEN[SCEN != ref_scen]
  calc_scen_index <- which(colnames(x_deaths) %in% calc_scen)

  ref_injuries <- as.data.frame(cbind(x_deaths[,1:2],
                                      deaths = x_deaths[[ref_scen]],
                                      ylls = x_yll[[ref_scen]]))
  deaths <- t(repmat(unlist(ref_injuries$deaths), NSCEN, 1)) - x_deaths[,calc_scen_index,drop = F]
  ylls <- t(repmat(unlist(ref_injuries$ylls),NSCEN,1)) - x_yll[,calc_scen_index,drop = F]
  deaths_yll_injuries <- as.data.frame(cbind(as.data.frame(x_deaths[,1:2]),deaths, ylls))

  metric <- c("deaths", "yll")
  k <- 1
  for  (i in 1:2)
    for (j in c(1:(NSCEN + 1))[-ref_scen_index]) {
      names(deaths_yll_injuries)[2 + k] <- paste0(SCEN_SHORT_NAME[j],"_",metric[i],"_inj")
      k <- k + 1
    }

  list(deaths_yll_injuries = deaths_yll_injuries,ref_injuries = ref_injuries)
}