R/calcAnimalStocks.R

In pik-piam/moinput: Model Operations Input Data Library

#' @title calcAnimalStocks
#' @description calculates stocks of animals of different categories.
#'
#' @param grouping IPCC: Animal grouping of IPCC Guidelines
#'
#' @return List of magpie objects with results on country level, weight on country level, unit and description.
#' @author Benjamin Leon Bodirsky
#' @seealso
#' \code{\link{calcExcretionIPCC}},
#' \code{\link{readIPCC}}
#' @examples
#' 
#' \dontrun{ 
#' calcOutput("AnimalStocks")
#' }
#' @importFrom magclass setNames


calcAnimalStocks<-function(grouping="IPCC"){
  
  if(grouping!="IPCC"){stop("so far only IPCC categories implemented.")}
  
  market_swine_share=0.9 # table 10.19
  
  LiveHead<-dimSums(readSource("FAO","LiveHead"),dim="ElementShort")
  LivePrim<-readSource("FAO","LivePrim")
  years<-intersect(getYears(LiveHead),getYears(LivePrim))
  LiveHead<-LiveHead[,years,]
  LivePrim<-LivePrim[,years,]
  
  # estimate numbers of animals for IPCC categories
  animals<-NULL
  
  # Dairy cows
  animals<-mbind(animals,setNames(collapseNames(LivePrim[,,c("Milk_Animals_(Head)")]
                      [,,c("882|Milk, whole fresh cow")]),"dairy cows"))
  # Other cattle
  animals<-mbind(animals,setNames(
    collapseNames(LiveHead[,,c("866|Cattle")])
    -setNames(animals[,,"dairy cows"],NULL)
  ,"other cattle"))
  
  # Dairy Buffalo
  animals<-mbind(animals,setNames(collapseNames(LivePrim[,,c("Milk_Animals_(Head)")]
                                                [,,c("951|Milk, whole fresh buffalo")]),"dairy buffalo"))
  # Other buffalo
  animals<-mbind(animals,setNames(
    collapseNames(LiveHead[,,c("946|Buffaloes")])
    -setNames(animals[,,"dairy buffalo"],NULL)
    ,"other buffalo"))

  # Market Swine
  animals<-mbind(animals,setNames(
    collapseNames(LiveHead[,,c("1034|Pigs")])
    *market_swine_share
    ,"market swine"))
  
  # Breeding Swine
  animals<-mbind(animals,setNames(
    collapseNames(LiveHead[,,c("1034|Pigs")])
    *(1-market_swine_share)
    ,"breeding swine"))

  # Dairy Sheep
  animals<-mbind(animals,setNames(collapseNames(LivePrim[,,c("Milk_Animals_(Head)")]
                                                [,,c("982|Milk, whole fresh sheep")]),"dairy sheep"))
  # Other sheep
  animals<-mbind(animals,setNames(
    collapseNames(LiveHead[,,c("976|Sheep")])
    -setNames(animals[,,"dairy sheep"],NULL)
    ,"other sheep"))
  
  # Dairy Goats
  animals<-mbind(animals,setNames(collapseNames(LivePrim[,,c("Milk_Animals_(Head)")]
                                                [,,c("1020|Milk, whole fresh goat")]),"dairy goats"))
  # Other goats
  animals<-mbind(animals,setNames(
    collapseNames(LiveHead[,,c("1016|Goats")])
    -setNames(animals[,,"dairy goats"],NULL)
    ,"other goats"))
  
  # Camels
  animals<-mbind(animals,setNames(collapseNames(LivePrim[,,c("Milk_Animals_(Head)")]
                                                [,,c("1130|Milk, whole fresh camel")]),"dairy camels"))
  # Other Camelids
  animals<-mbind(animals,setNames(
    dimSums(LiveHead[,,c("1126|Camels","1157|Camelids, other")],dim=3.1)
    -setNames(animals[,,"dairy camels"],NULL)
    ,"other camels"))
  
  # Horses
  animals<-mbind(animals,setNames(
    collapseNames(LiveHead[,,c("1096|Horses")])
    ,"horses"))
   
  # Mules/Asses
  animals<-mbind(animals,setNames(
    dimSums(LiveHead[,,c("1107|Asses","1110|Mules")],dim=3.1)
    ,"mules and asses"))
  
  # Poultry Layers
  animals<-mbind(animals,setNames(collapseNames(dimSums(LivePrim[,,c("Laying_(Head)")]
                                                [,,c("1062|Eggs, hen, in shell","1091|Eggs, other bird, in shell")],dim=3.1)),"poultry layers"))
  # Broilers
  animals<-mbind(animals,setNames(
    dimSums(LiveHead[,,c("1057|Chickens","1083|Pigeons, other birds")],dim=3.1)
    -setNames(animals[,,"poultry layers"],NULL)
    ,"broilers"))
  
  # Turkey
  animals<-mbind(animals,setNames(
    dimSums(LiveHead[,,c("1072|Geese and guinea fowls", "1079|Turkeys" )],dim=3.1)
    ,"turkey"))
  
  # Ducks
  animals<-mbind(animals,setNames(
    collapseNames(LiveHead[,,c("1068|Ducks")])
    ,"ducks"))
  
  # ignore
  # "1140|Rabbits and hares","1150|Rodents, other"   
  animals=animals/1000000
  
  #sort according to n_rate animal categories
  
  
  # remove all negative values
  remove <- which(animals<0)
  
  if(length(remove)>0){
    vcat(2, paste0(length(remove)," negative values removed"))
    animals[remove] <-0
  }

  return(list(x=animals,
              weight=NULL,
              unit="Million animals",
              description="Animal stocks, for laying hens and dairy cattle producing animals",
              min=0)
  )                   
}