Skip to contents

Set up biological parameter inputs for closed-loop simulation

Setup_Sim_Biologicals.Rd

Populates a simulation list (created by Setup_Sim_Dim) with biological arrays needed to run the operating model: natural mortality, weight-at-age (spawning, fishery, and survey), maturity-at-age, ageing error, and an optional size-age transition matrix for length compositions. All arrays must conform to the dimension structure stored in sim_list.

Usage

Setup_Sim_Biologicals(
  sim_list,
  natmort_input,
  WAA_input,
  WAA_fish_input,
  WAA_srv_input,
  MatAA_input,
  AgeingError_input = NULL,
  AgeingError_fish_input = NULL,
  AgeingError_srv_input = NULL,
  SizeAgeTrans_input = NULL,
  SizeAgeTrans_fish_input = NULL,
  SizeAgeTrans_srv_input = NULL
)

Arguments

sim_list

Simulation list object returned by Setup_Sim_Dim, which defines the dimension sizes used to validate all input arrays.

natmort_input

Natural mortality array, either [n_pop × n_regions × n_yrs × n_ages × n_sexes × n_sims] or [n_pop × n_regions × n_yrs × n_seas × n_ages × n_sexes × n_sims]. Values are instantaneous rates per year in both forms, and the mortality applied within a season is the rate times seasdur.

WAA_input

Spawning weight-at-age array with dimensions [n_pop × n_regions × n_yrs × n_seas × n_ages × n_sexes × n_sims]. Used to compute spawning stock biomass.

WAA_fish_input

Fishery weight-at-age array with dimensions [n_pop × n_regions × n_yrs × n_seas × n_ages × n_sexes × n_fish_fleets × n_sims]. Used to compute fishery biomass and catch in weight.

WAA_srv_input

Survey weight-at-age array with dimensions [n_pop × n_regions × n_yrs × n_seas × n_ages × n_sexes × n_srv_fleets × n_sims]. Used to compute survey biomass indices.

MatAA_input

Maturity-at-age array with dimensions [n_pop × n_regions × n_yrs × n_seas × n_ages × n_sexes × n_sims]. Values should be proportions in \([0, 1]\). When rec_lag = 0 (age-0 recruitment, set via Setup_Sim_Rec), maturity at the recruit age (the first age class) must be exactly 0 for all populations, regions, years, seasons, and sexes. An error is raised otherwise.

AgeingError_input

Ageing error (age-length transition) array with dimensions [n_yrs × n_model_ages × n_obs_ages × n_sims], where each [n_model_ages × n_obs_ages] slice is a row-stochastic matrix mapping true modeled ages to observed age bins. If NULL (default), an identity matrix is constructed for each year and simulation, which assumes that modeled and observed age bins are identical in number and alignment. If observed age bins are a subset of modeled ages (e.g., observed ages 2-10 vs. modeled ages 1-10), the default identity matrix will cause a dimensional mismatch. In that case, supply a shifted identity matrix such as diag(1, n_model_ages)[, obs_age_index] to correctly drop or collapse model ages into observed bins.

AgeingError_fish_input

Optional fleet-specific ageing error for the simulated fishery fleets, dimensioned [n_yrs × n_ages × n_obs_ages × n_fish_fleets × n_sims], or NULL (default) to give every fishery fleet AgeingError_input.

AgeingError_srv_input

Optional fleet-specific ageing error for the simulated survey fleets, dimensioned [n_yrs × n_ages × n_obs_ages × n_srv_fleets × n_sims], or NULL (default) to give every survey fleet AgeingError_input.

SizeAgeTrans_input

Size-age transition matrix array with dimensions [n_pop × n_regions × n_yrs × n_seas × n_lens × n_ages × n_sexes × n_sims]. Each slice maps age classes to length bins and should be column-stochastic (columns sum to 1). Only required when fitting length compositions; defaults to NULL.

SizeAgeTrans_fish_input, SizeAgeTrans_srv_input

Optional size-age transition arrays per fleet, [n_pop x n_regions x n_yrs x n_seas x n_lens x n_ages x n_sexes x n_fleets x n_sims], each read at that fleet's own timing. When supplied they are used for that fleet type in place of SizeAgeTrans_input; the self-test passes the fitted model's own keys here when growth was estimated.

Value

The input sim_list with the following fields added or updated:

$natmort

Natural mortality array.

$WAA

Spawning weight-at-age array.

$WAA_fish

Fishery weight-at-age array.

$WAA_srv

Survey weight-at-age array.

$MatAA

Maturity-at-age array.

$AgeingError

Ageing error array (identity matrix if not supplied).

$SizeAgeTrans

Size-age transition array (only added if supplied).

See also

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