R/fixed_bmsy.R

In SPRFMO/jjmr: Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model

#' Calculate or input a fixed Bmsy value for the jjm model
#' Updates the msy_mt table in the jjm output with new B/Bmsy ratios.
#'
#' @param mod jjm object that is a list of lists
#' @param refpt A number to input as Bmsy. If not filled, calculated as the average of the Bmsy estimated for the last ten years (as determined in SCW14 benchmark 2022)
#' @return A model
#' @examples
#' # fixed_bmsy(mod_h1_1.00, refpt=5500) # To input a fixed Bmsy
#' # fixed_bmsy(mod_h1_1.00) # To calculate the Bmsy
#' @export

fixed_bmsy <- function(mod, refpt=NULL){
	for(s in 1:mod[[1]]$info$output$nStock) {
		
		if(is.null(refpt)) {newrefpt <- mean(rev(mod[[1]]$output[[s]]$msy_mt[,10])[1:10])}
			else{newrefpt <- refpt}
	  	mod[[1]]$output[[s]]$oldbmsy <- mod[[1]]$output[[s]]$msy_mt[,10]
	  	old_rat <- (mod[[1]]$output[[s]]$msy_mt[,13])
	  	new_rat <- (mod[[1]]$output[[s]]$msy_mt[,12]/ newrefpt)
	  	mod[[1]]$output[[s]]$msy_mt[,13] <- new_rat
	  	mod[[1]]$output[[s]]$msy_mt[,10] <- newrefpt
	  }
  return(mod)
}