calc_ref: Reference points

In salmonMSE: Management Strategy Evaluation for Salmon Species

Reference points

Description

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"), AEQ = TRUE)

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"),
  AEQ = TRUE,
  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).
AEQ	Logical, whether to maximize preterminal catch in terms of adult equivalents
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

See Also

calc_Smsy_Ricker()

Examples

ref_simple <- calc_ref(simple_SOM)
ref_multi <- calc_ref(multi_SOM)

salmonMSE documentation built on Aug. 20, 2026, 5:09 p.m.