Simulate the fishery dynamics for a short-lived semelparous species

Simulate the fishery dynamics for a short-lived semelparous species

Simulate(
  LifeHistory = NULL,
  Exploitation = NULL,
  nsim = 100,
  seed = 101,
  currentYr = format(Sys.Date(), "%Y"),
  silent = FALSE
)

Arguments

LifeHistory

A named list object with the life-history parameters, or the file path to a correctly formatted CSV file containing the LifeHistory (and optionally Exploitation) parameters. The LifeHistory object can optionally include the Exploitation parameters as well.

Exploitation

An named list object with the exploitation parameters or the file path to a correctly formatted Exploitation CSV file. Not needed if LifeHistory already includes the Exploitation parameters.

nsim

The number of stochastic simulations. Default is 100.

seed

The seed for the random number generator

currentYr

The current (most recent) year for the simulations

silent

Hide messages?

Value

A named list of class Simulation containing:

• LifeHistory: The LifeHistory Object used for the simulations

• Exploitation: The Exploitation Object used for the simulations, with the addition of Sel_at_Age (selectivity schedule)

• At_Age_Time_Series: A data frame with the following columns

  • Sim: The simulation number

  • Age: The age class

  • Year: The year

  • Month: Abbreviated calendar month

  • Month_ind: Numerical index for the monthly timestep

  • N_fished: The number of fished animals in each age class for each timestep

  • N_unfished: The number of unfished animals in each age class for each timestep

  • N_unfished_eq: The equilibrium number of unfished animals in each age class for each timestep

  • B_fished: The biomass of fished animals in each age class for each timestep

  • B_unfished: The biomass of unfished animals in each age class for each timestep

  • SB_fished: The spawning biomass of fished animals in each age class for each timestep

  • SB_unfished: The spawning biomass of unfished animals in each age class for each timestep

  • Catch: The catch biomass in each age class for each timestep

  • Catch_n: The catch numbers in each age class for each timestep

• Time_Series: A data frame with the following columns

  • Sim: The simulation number

  • Year: The year

  • Month: Abbreviated calendar month

  • Month_ind: Numerical index for the monthly timestep

  • N_fished: The total number of fished animals in each timestep

  • N_unfished: The total number of unfished animals in each timestep

  • B_fished: The biomass of fished animals in each timestep

  • B_unfished: The biomass of unfished animals in each timestep

  • SB_fished: The spawning biomass of fished animals in each timestep

  • SB_unfished: The spawning biomass of unfished animals in each timestep

  • Catch: The catch biomass in each timestep

  • Recruits: The number of recruits in each timestep

  • SPR: The equilibrium spawning potential ratio in each timestep

  • Effort: The fishing effort in each timestep

  • F_mort: The fishing mortality in each timestep

  • Rec_Devs: The recruitment deviation in each timestep

Details

See the example SLAM::LifeHistory and SLAM::Exploitation objects and help documentation (?LifeHistory and ?Exploitation) for examples.