R/calcNitrogenBudgetOcean.R

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

#' @title calcNitrogenBudgetOcean
#' @description Calculates Nitrogen Budgets for Oceans on global level. Values are placed in Antarcica (ATA)
#' @param deposition Method for calculating Atmospheric deposition: Nsurplus2 and Nsurplus are based on
#' deposition rates based on own emission calculations after 2 or after 1 iteration, respectively.
#' @param leaching Method for calculating leaching: Nsurplus2 and Nsurplus are based on
#' deposition rates based on own emission calculations after 2 or after 1 iteration, respectively.
#' @return List of magpie object with results on country level, weight on country level, unit and description.
#' @author Benjamin Leon Bodirsky
#' @examples
#' \dontrun{
#' calcOutput("NitrogenBudgetOcean")
#' }
#' @importFrom magclass setNames


calcNitrogenBudgetOcean <- function(deposition = "ACCMIP", leaching = "Nsurplus") {
  vcat(2, "strange to change leaching attribute in if statement. Is this correct?")
  past <- findset("past")
  dep <- calcOutput("AtmosphericDeposition", datasource = deposition, glo_incl_oceans = FALSE,
                    cellular = FALSE, emission = FALSE, aggregate = FALSE)
  depGlo <- calcOutput("AtmosphericDeposition", datasource = deposition, glo_incl_oceans = TRUE,
                       cellular = FALSE, emission = FALSE, aggregate = FALSE)

  deposition <- (dimSums(depGlo, dim = 3) - dimSums(dep, dim = c(1, 3)))[, past, ]

  if (leaching == "Nsurplus") {
    groundwater <- dimSums(calcOutput("EmisNitrogenPast", method = "IPCC", aggregate = FALSE)[, , "no3_n"],
                           dim = c(3.1, 3.2))
  } else if (leaching == "Nsurplus2") {
    groundwater <- dimSums(calcOutput("EmisNitrogenPast", method = "Nsurplus", aggregate = FALSE)[, , "no3_n"],
                           dim = c(3.1, 3.2))
  }

  sewage <- collapseNames(calcOutput("NutrientBudgetSewage", aggregate = FALSE)[, , "nr"][, , "freshwater"])

  waterloss <- calcOutput("EmisNitrogenWater", method = leaching, aggregate = FALSE)
  fish <- collapseNames(calcOutput("FAOmassbalance", aggregate = FALSE)[, past, "fish"][, , "production"][, , "nr"])

  riverdischarge <- setNames(groundwater + sewage - dimSums(waterloss, dim = 3), "riverdischarge")

  budget <- add_columns(riverdischarge, addnm = c("fixation_ocean", "deposition", "fish", "surplus"))
  budget[, , c("fixation_ocean", "deposition", "fish", "surplus")] <- 0
  budget[, , "fish"] <- fish
  # 140 Tg: Voss, M. et al. The marine nitrogen cycle: recent discoveries,
  # uncertainties and the potential relevance of climate change. Philosophical Transactions of the Royal
  # Society B: Biological Sciences 368, 20130121–20130121 (2013).
  budget["ATA", , "fixation_ocean"] <- 140
  budget["ATA", , "deposition"] <- deposition
  budget["ATA", , "surplus"] <- dimSums(budget[, , c("fixation_ocean", "deposition")], dim = c(1, 3)) -
    dimSums(budget[, , c("fish")], dim = c(1, 3))

  vcat(2, "Fish production is allocated to oceans, but happens in both Oceans and Inland water bodies")

  return(list(
    x = budget,
    weight = NULL,
    unit = "Mt Nr",
    description = "Nitrogen budget for oceans"))
}