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Setup values and dimensions of fishing processes

Setup_Sim_Fishing.Rd

Setup values and dimensions of fishing processes

Usage

Setup_Sim_Fishing(
  sim_list,
  ln_sigmaC = array(log(0.02), dim = c(sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_fish_fleets)),
  init_F_val = 0,
  Fmort_input = array(0.1, dim = c(sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_fish_fleets, sim_list$n_sims)),
  fish_sel_input,
  fish_q_input = array(1, dim = c(sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_fish_fleets, sim_list$n_sims)),
  ObsFishIdx_SE = array(0.2, dim = c(sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_fish_fleets)),
  fish_idx_type = rep(1, sim_list$n_fish_fleets),
  comp_fishage_like = rep(0, sim_list$n_fish_fleets),
  ISS_FishAgeComps = array(100, dim = c(sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_sexes, sim_list$n_fish_fleets, sim_list$n_sims)),
  ln_FishAge_theta = array(log(1), dim = c(sim_list$n_regions, sim_list$n_sexes,
    sim_list$n_fish_fleets)),
  ln_FishAge_theta_agg = rep(log(1), sim_list$n_fish_fleets),
  FishAge_corr_pars_agg = rep(0.01, sim_list$n_fish_fleets),
  FishAge_corr_pars = array(0.01, dim = c(sim_list$n_regions, sim_list$n_sexes,
    sim_list$n_fish_fleets, 2)),
  FishAgeComps_Type = array(2, dim = c(sim_list$n_yrs, sim_list$n_fish_fleets)),
  comp_fishlen_like = rep(0, sim_list$n_fish_fleets),
  ISS_FishLenComps = array(100, dim = c(sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_sexes, sim_list$n_fish_fleets, sim_list$n_sims)),
  ln_FishLen_theta = array(log(1), dim = c(sim_list$n_regions, sim_list$n_sexes,
    sim_list$n_fish_fleets)),
  ln_FishLen_theta_agg = rep(log(1), sim_list$n_fish_fleets),
  FishLen_corr_pars_agg = rep(0.01, sim_list$n_fish_fleets),
  FishLen_corr_pars = array(0.01, dim = c(sim_list$n_regions, sim_list$n_sexes,
    sim_list$n_fish_fleets, 2)),
  FishLenComps_Type = array(2, dim = c(sim_list$n_yrs, sim_list$n_fish_fleets))
)

Arguments

sim_list

Simulation list object from `Setup_Sim_Dim()`

ln_sigmaC

Observation error for catch [n_regions × n_yrs × n_fish_fleets] (default: `log(0.02)`)

init_F_val

Initial fishing mortality value (default: `0`)

Fmort_input

Fishing mortality input array [n_regions × n_yrs × n_fish_fleets × n_sims] (default: `0.1`)

fish_sel_input

Fishery selectivity array [n_regions × n_yrs × n_ages × n_sexes × n_fish_fleets × n_sims] (no default, must be provided)

fish_q_input

Fishery catchability array [n_regions × n_yrs × n_fish_fleets × n_sims] (default: `1`)

ObsFishIdx_SE

Observation error of fishery index [n_regions × n_yrs × n_fish_fleets] (default: `0.2`)

fish_idx_type

Vector of index types [n_fish_fleets] (default: all `1` = biomass index)

  • 0: Abundance index

  • 1: Biomass index

comp_fishage_like

Vector [n_fish_fleets] specifying likelihood for simulating age comps (default: all `0` = multinomial)

  • 0: Multinomial

  • 1: Dirichlet-Multinomial

  • 2: Logistic Normal iid

  • 3: Logistic Normal 1dar1

  • 4: Logistic Normal 2d correlation (constant by sex, 1dar1 by age)

ISS_FishAgeComps

Input sample sizes [n_regions × n_yrs × n_sexes × n_fish_fleets × n_sims] (default: `100`)

ln_FishAge_theta

Overdispersion parameters [n_regions × n_sexes × n_fish_fleets] (default: `log(1)`)

ln_FishAge_theta_agg

Overdispersion parameters for aggregated comps [n_fish_fleets] (default: `log(1)`)

FishAge_corr_pars_agg

Correlation parameters (agg.) for options 3–4 [n_fish_fleets] (default: `0.01`)

FishAge_corr_pars

Correlation parameters [n_regions × n_sexes × n_fish_fleets x 2] (default: `0.01`)

FishAgeComps_Type

Array [n_yrs × n_fish_fleets] (default: `2` = joint by sex, split by region)

  • 0: Aggregated

  • 1: Split by sex and region

  • 2: Joint by sex, split by region

  • 999: Not simulated

comp_fishlen_like

Vector [n_fish_fleets] specifying likelihood for simulating length comps (default: all `0` = multinomial)

  • 0: Multinomial

  • 1: Dirichlet-Multinomial

  • 2: Logistic Normal iid

  • 3: Logistic Normal 1dar1

  • 4: Logistic Normal 2d correlation (constant by sex, 1dar1 by length)

ISS_FishLenComps

Input sample sizes [n_regions × n_yrs × n_sexes × n_fish_fleets × n_sims] (default: `100`)

ln_FishLen_theta

Overdispersion parameters [n_regions × n_sexes × n_fish_fleets x 2] (default: `log(1)`)

ln_FishLen_theta_agg

Overdispersion parameters for aggregated comps [n_fish_fleets] (default: `log(1)`)

FishLen_corr_pars_agg

Correlation parameters (agg.) for options 3–4 [n_fish_fleets] (default: `0.01`)

FishLen_corr_pars

Correlation parameters [n_regions × n_sexes × n_fish_fleets] (default: `0.01`)

FishLenComps_Type

Array [n_yrs × n_fish_fleets] (default: `2` = joint by sex, split by region)

  • 0: Aggregated

  • 1: Split by sex and region

  • 2: Joint by sex, split by region

  • 999: Not simulated

See also

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