R/Auxiliary_Functions_Calculations_exem.R

In ElsevierSoftwareX/SOFTX-D-15-00067: Bio-Economic Impact Assessment of Management strategies using FLR

# Dorleta Garcia 2015/01/14
# Functions
#
# overfishing: Are the stock suffering of overfishing, returns a matrix [nst,nit]

#-------------------------------------------------------------------------------------------
# overfishing: Are the stock suffering of overfishing, returns a matrix [nst,nit]
#-------------------------------------------------------------------------------------------
overfishing <- function(biols, fleets, advice.ctrl, year){
  if(is.numeric(year)) year <- dimnames(biols[[1]]@n)[[2]][year]
  obj <- list(biols = biols, fleets = fleets)
  f    <- F_flbeia(obj, years = year)
  

  
  fmsy <- numeric(length(biols))
  names(fmsy) <- names(biols)
  
  for(st in names(biols)){
    Fref <- dimnames(advice.ctrl[[st]]$ref.pts)[[1]]
    Fref <- Fref[which(substr(Fref, 1,1) == 'F')] 
    
    if (length(Fref)>0){
      if(length(dim(advice.ctrl[[st]]$ref.pts)) == 3) Fref <-  advice.ctrl[[st]]$ref.pts[Fref,year,]
      if(length(dim(advice.ctrl[[st]]$ref.pts)) == 2) Fref <- advice.ctrl[[st]]$ref.pts[Fref,]
      if(length(dim(advice.ctrl[[st]]$ref.pts)) == 1) Fref <- advice.ctrl[[st]]$ref.pts[Fref]   
    }
    
    

      
    fmsy[st] <- ifelse(is.null(Fref), NA, Fref)
  }

  
  res <- sapply(names(fmsy), function(x) fmsy[x] < f[x,,])
  res <- ifelse(is.na(res), FALSE, res)
  if(!is.null(dim(res))) res <- t(res) # if there are iterations put them in columns not in rows.
  
  res <- as.matrix(res, nrow = (length(biols)))
  rownames(res) <- names(biols) 
  return(res)  
}