get_SSB: Calculate Spawning Stock Biomass (SSB) or total biomass

In CefasRepRes/LeMaRns: Length-Based Multispecies Analysis by Numerical Simulation

Calculate Spawning Stock Biomass (SSB) or total biomass

Description

Calculates the Spawning Stock Biomass (SSB) or the total biomass of each species in the model.

Usage

get_SSB(inputs, outputs, ...)

## S4 method for signature 'LeMans_param,LeMans_outputs'
get_SSB(
  inputs,
  outputs,
  species = 1:dim(outputs@N)[2],
  time_steps = 1:dim(outputs@N)[3]
)

## S4 method for signature 'LeMans_param,missing'
get_SSB(inputs, N, species = 1:dim(N)[2], time_steps = 1:dim(N)[3])

## S4 method for signature 'missing,LeMans_outputs'
get_SSB(
  wgt,
  mature,
  outputs,
  species = 1:dim(outputs@N)[2],
  time_steps = 1:dim(outputs@N)[3],
  species_names = NULL
)

## S4 method for signature 'missing,missing'
get_SSB(
  wgt,
  mature,
  N,
  species = 1:dim(N)[2],
  time_steps = 1:dim(N)[3],
  species_names = NULL
)

get_biomass(inputs, outputs, ...)

## S4 method for signature 'LeMans_param,LeMans_outputs'
get_biomass(
  inputs,
  outputs,
  species = 1:dim(outputs@N)[2],
  time_steps = 1:dim(outputs@N)[3]
)

## S4 method for signature 'LeMans_param,missing'
get_biomass(inputs, N, species = 1:dim(N)[2], time_steps = 1:dim(N)[3])

## S4 method for signature 'missing,LeMans_outputs'
get_biomass(
  wgt,
  outputs,
  species = 1:dim(outputs@N)[2],
  time_steps = 1:dim(outputs@N)[3],
  species_names = NULL
)

## S4 method for signature 'missing,missing'
get_biomass(
  wgt,
  N,
  species = 1:dim(N)[2],
  time_steps = 1:dim(N)[3],
  species_names = NULL
)

Arguments

inputs	A LeMans_param object containing the parameter values of the current LeMans model.
outputs	A LeMans_outputs object containing the outputs of the model run.
...	Additional arguments.
species	A numeric value or vector or a character string or vector of the species that you wish to calculate the mean maximum length. The default is 1:dim(N)[2].
time_steps	A numeric vector of the time steps that you wish to calculate the mean maximum length. The default is 1:dim(N)[3].
N	An array with dimensions nsc, nfish and tot_time representing the number of individuals in each length class for each time step.
wgt	A matrix with dimensions nsc and nfish representing the weight of each species in each length class.
mature	A matrix with dimensions ncs and nfish with elements in the range 0-1 representing the proportion of mature individuals of each species in each length class.
species_names	A character vector of length nfish that denotes the names of the species in the model.

Details

The SSB for each species in species is equal to:

colSums(N[, species]*wgt[, species]*mature[, species]).

The biomass for each species in species is equal to:

colSums(N[, species]*wgt[, species])

Value

If length(species)>1, get_SSB returns a matrix with dimensions length(time_steps) by length(species) where the i,jth element is the SSB (g) of the jth species in the ith time_steps. If length(species)==1, the function will return a numeric vector of length length(time_steps).

If length(species)>1, get_biomass returns a matrix with dimensions length(time_steps) by length(species) where the i,jth element is the biomass (g) of the jth species in the ith time_steps. If length(species)==1, the function will return a numeric vector of length length(time_steps).

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
get_SSB(inputs=NS_params, outputs=model_run)

# Calculate biomass
get_biomass(inputs=NS_params, outputs=model_run)

CefasRepRes/LeMaRns documentation built on Jan. 27, 2023, 4:01 p.m.