Reference points

Calculate MSY and Sgen reference points for the operating model. Uses the biological parameters (maturity, natural mortality) in the last year of the projection.

calc_MSY() calculates the MSY reference points from a set of biological and fishery parameters
calc_Sgen() calculates the Sgen, the spawner abundance that would reach the spawner abundance at MSY after one generation without fishing
calc_ref() is a wrapper function that calculates MSY and Sgen for an operating model

Usage

calc_ref(SOM, rel_F, check = TRUE, maximize = c("MSY", "MER"))

calc_MSY(
  Mjuv,
  fec,
  p_female,
  rel_F,
  vulPT,
  vulT,
  p_mature,
  s_enroute,
  n_g = 1,
  p_LHG = 1,
  SRRpars,
  maximize = c("MSY", "MER"),
  F_search = c(1e-08, 5)
)

calc_Sgen(
  Mjuv,
  fec,
  p_female,
  rel_F,
  vulPT,
  vulT,
  p_mature,
  s_enroute,
  n_g = 1,
  p_LHG = 1,
  SRRpars,
  SMSY,
  F_search = c(1e-08, 100),
  nyears
)

Arguments

SOM: An object of class SOM
rel_F: Numeric length 2, indicates the relative effort in the preterminal and terminal fisheries, with a maximum value of 1. The default is c(0, 1) which indicates a yield calculation with only the terminal fishery.
check: Logical, whether to check the SOM object using check_SOM()
maximize: Character, whether the MSY calculation is the optimum that maximizes catch ("MSY") or excess recruitment ("MER"). The two methods should be equivalent when rel_F = c(0, 1).
Mjuv: Numeric maxage for juvenile natural mortality. Can be a matrix [maxage, n_g].
fec: Numeric maxage for fecundity. Can be a matrix [maxage, n_g].
p_female: Numeric for proportion female spawners
vulPT: Numeric maxage for preterminal vulnerability at age
vulT: Numeric maxage for terminal vulnerability at age
p_mature: Numeric maxage for maturity proportions at age. Can be a matrix [maxage, n_g].
s_enroute: Numeric for en-route survival of escapement to spawning grounds
n_g: Integer, number of life history groups within a cohort
p_LHG: Numeric n_g for proportion of the total egg production assigned to each life history group within a cohort
SRRpars: Data frame, one row, that contains the stock recruit parameters that predicts density-dependent survival at the egg-smolt life stage
F_search: Numeric, length 2 for the range of F values to search for the instantaneous fishing mortality that produces MSY
SMSY: Numeric, spawning abundance at MSY
nyears: Integer, number of years to project the population with no fishing to reach SMSY. Default is the minimum age of maturity.

Value

calc_MSY returns a vector of various state variables (catch, exploitation rate, egg production, spawners) at MSY
calc_Sgen returns a numeric
calc_ref returns a list by stock, each containing a matrix of MSY state variables and Sgen by simulation

Usage

Arguments

Value

See also