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Set up recruitment dynamics for simulation

Setup_Sim_Rec.Rd

Set up recruitment dynamics for simulation

Usage

Setup_Sim_Rec(
  do_recruits_move = 0,
  sexratio_input = array(if (sim_list$n_sexes == 1) 1 else 0.5, dim =
    c(sim_list$n_regions, sim_list$n_yrs, sim_list$n_sexes, sim_list$n_sims)),
  R0_input = array(10, dim = c(sim_list$n_regions, sim_list$n_yrs, sim_list$n_sims)),
  h_input = array(0.8, dim = c(sim_list$n_regions, sim_list$n_yrs, sim_list$n_sims)),
  ln_sigmaR = log(c(1, 1)),
  recruitment_opt = "bh_rec",
  rec_dd = "global",
  init_dd = "global",
  sim_list,
  init_age_strc = 2,
  t_spawn = 0,
  rec_lag = 1,
  Rec_input = NULL,
  ln_InitDevs_input = NULL
)

Arguments

do_recruits_move

Indicator for whether recruits move (default = 0):

  • 0: No movement

  • 1: Move

sexratio_input

Sex ratio array [n_regions × n_yrs × n_sexes × n_sims] (default = 1 if one sex, else 0.5 for each sex)

R0_input

Unfished recruitment (R0) array [n_regions × n_yrs × n_sims] (default = 10)

h_input

Steepness array [n_regions × n_yrs × n_sims] (default = 0.8)

ln_sigmaR

Logarithmic standard deviation of recruitment [2]: 1st = sigma for initial devs, 2nd = sigma for latter devs (default = log(c(1, 1)))

recruitment_opt

Recruitment type (default = "bh_rec"):

  • "mean_rec": Mean recruitment

  • "bh_rec": Beverton-Holt recruitment

  • "resample_from_input": Resampling recruitment years from `Rec_input` and preserves covariance of recruitment among regions if spatially-explicit values are provided

rec_dd

Recruitment density dependence (default = "global"):

  • "global": Shared across regions

  • "local": Region-specific

init_dd

Initial age density dependence (default = "global"):

  • "global": Shared across regions

  • "local": Region-specific

sim_list

Simulation list object from `Setup_Sim_Dim()`

init_age_strc

Integer flag specifying initialization of initial age structure:

  • 0: Initialize by iteration.

  • 1: Initialize using a scalar geometric series (does not account for movement).

  • 2: Initialize using a matrix geometric series (accounts for movement; default).

t_spawn

Spawn timing fraction of the year (scalar, default = 0)

rec_lag

Recruitment lag (default = 1)

Rec_input

Recruitment array [n_regions × n_yrs × n_sims] (default = NULL)

ln_InitDevs_input

Initial deviations [n_regions × (n_ages-1) × n_sims] (default = NULL)

See also

Other Simulation Setup: Setup_Sim_Biologicals(), Setup_Sim_Containers(), Setup_Sim_Dim(), Setup_Sim_Fishing(), Setup_Sim_Survey(), Setup_Sim_Tagging(), Setup_sim_env(), Simulate_Pop_Static(), run_annual_cycle(), simulation_data_to_SPoRC(), simulation_self_test()