R/forest.mortality.r

In nuaquilue/SBW: Spruce budworm outbreaks model

#' Forest mortality by SBW
#'
#' Determines the cells killed by recurrent SBW defoliation
#' 
#' @param land A \code{landscape} data frame with forest stand records in rows
#'
#' @return A vector with the \code{cell.id} of the forest cells killed by 
#' recurrent SBW defoliation according to species composition
#' 
#' @export
#' 
#' @examples
#' data(landscape)
#' forest.mortality(landscape)
#' 



forest.mortality = function(land){
  
  ## Prob.mortality in cell c = number of years of defoliation in cell c, and species composition in cell c   
  ## (exemple de paramètres: par ex for SAB: 5-7 years = prob 10% per year, 7-10 = 15%, >10 20%; 
  ## for EPN: 5-7 years = 0%, 7-10= 5 %, >10 = 10%)
  
  ## Vector to store cell.id of killed cells
  kill.cells = numeric()
  
  ## Low mortality of Balsam fir
  target = filter(land, spp=="SAB", ny.def>=5, ny.def<=7)
  # size = pmin(nrow(target)*0.1, sum(target$curr.intens.def>0))
  if(nrow(target)>1)
    aux = sample(target$cell.id, size=nrow(target)*0.1, replace=F, 
                  prob=pmax(target$cum.intens.def*target$curr.intens.def, target$cum.intens.def))
  else
    aux = target$cell.id
  kill.cells = c(kill.cells,aux)
  
  ## Medium mortality of Balsam fir
  target = filter(land, spp=="SAB", ny.def>=8, ny.def<=10)
  if(nrow(target)>1)
    aux = sample(target$cell.id, size=nrow(target)*0.15, replace=F, 
                  prob=pmax(target$cum.intens.def*target$curr.intens.def, target$cum.intens.def))
  else
    aux = target$cell.id
  kill.cells = c(kill.cells,aux)
  
  ## High mortality of Balsam fir
  target = filter(land, spp=="SAB", ny.def>=11)
  if(nrow(target)>1)
    aux = sample(target$cell.id, size=nrow(target)*0.2, replace=F, 
                  prob=pmax(target$cum.intens.def*target$curr.intens.def, target$cum.intens.def))
  else
    aux = target$cell.id
  kill.cells = c(kill.cells,aux)
  
  ## Medium mortality of Black spruce
  target = filter(land, spp=="EPN", ny.def>=8, ny.def<=10)
  if(nrow(target)>1)
    aux = sample(target$cell.id, size=nrow(target)*0.05, replace=F, 
                  prob=pmax(target$cum.intens.def*target$curr.intens.def, target$cum.intens.def))
  else
    aux = target$cell.id
  kill.cells = c(kill.cells,aux)
  
  ## High mortality of Balsam fir
  target = filter(land, spp=="EPN", ny.def>=11)
  if(nrow(target)>1)
    aux = sample(target$cell.id, size=nrow(target)*0.1, replace=F, 
                  prob=pmax(target$cum.intens.def*target$curr.intens.def, target$cum.intens.def))
  else
    aux = target$cell.id
  kill.cells = c(kill.cells,aux)
  
  return(kill.cells)
  
}