R/calc_output.R

In LeMaRns: Length-Based Multispecies Analysis by Numerical Simulation

#' @include run_LeMans.R
#' @include param_setup.R
NULL


#' Calculate Spawning Stock Biomass (SSB) or total biomass
#'
#' @description Calculates the spawning stock biomass (SSB) or total biomass of each species in the model.
#' @param wgt A matrix with dimensions \code{nsc} and \code{nfish} representing the weight of each species in each length class.
#' @param mature A matrix with dimensions \code{ncs} and \code{nfish} with elements in the range 0-1 representing the proportion of mature individuals of each species in each length class.
#' @param N A matrix with dimensions \code{nsc} and \code{nfish} representing the number of individuals in each length class for the current time step.
#' @details The Spawning Stock Biomass is equal to \code{colSums(mature*N*wgt)} and the total biomass is equal to \code{colSums(mature*N*wgt)}.
#' @return \code{calc_SSB} returns a numeric vector of length \code{nfish} representing the SSB of each species (g).
#' @return \code{calc_biomass} returns a numeric vector of length \code{length(species)} where the \code{j}th element is the biomass (g) of the \code{j}th species.
#' @seealso \code{\link{calc_recruits}}
#' @examples
#' # Set up and run the model
#' NS_params <- LeMansParam(NS_par, tau=NS_tau, eta=rep(0.25, 21), L50=NS_par$Lmat, other=1e12)
#' effort <- matrix(0.5, 10, dim(NS_params@Qs)[3])
#' model_run <- run_LeMans(NS_params, years=10, effort=effort)
#'
#' # Calculate SSB
#' calc_SSB(wgt=NS_params@wgt, mature=NS_params@mature, N=model_run@N[,,101])
#'
#' # Calculate biomass in the last time step
#' calc_biomass(wgt=NS_params@wgt, N=model_run@N[,,101])
#' @export
calc_SSB <- function(wgt, mature, N) {
  SSB <- mature*N*wgt
  if (is.matrix(SSB)) {
    return(colSums(SSB))
  }
  return(sum(SSB))
}

#' @rdname calc_SSB
#' @export
calc_biomass <- function(wgt, N){
  biomass <- N*wgt
  if (is.matrix(biomass)){
    return(colSums(biomass))
  }
  return(sum(biomass))
}