Set up biological parameter inputs for closed-loop simulation

Sets natural mortality, weight-at-age, maturity-at-age, ageing error and an optional size-age transition for the operating model. All arrays are validated against the dimensions in sim_list. Call after Setup_Sim_Dim.

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,
  LenBinMap_input = NULL,
  CAAL_LenBinMap_input = NULL,
  SizeAgeTrans_input = NULL,
  SizeAgeTrans_fish_input = NULL,
  SizeAgeTrans_srv_input = NULL
)

Arguments

sim_list

Simulation list returned by Setup_Sim_Dim.

natmort_input

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

WAA_input

Spawning weight-at-age array [n_pop × n_regions × n_yrs × n_seas × n_ages × n_sexes × n_sims].

WAA_fish_input

Fishery weight-at-age array, WAA_input with an n_fish_fleets dim before the simulations.

WAA_srv_input

Survey weight-at-age array, WAA_input with an n_srv_fleets dim before the simulations.

MatAA_input

Maturity-at-age array dimensioned like WAA_input, in \([0, 1]\). Maturity at the first age must be exactly 0 under rec_lag = 0, set through Setup_Sim_Rec.

AgeingError_input

Ageing error array [n_yrs × n_model_ages × n_obs_ages × n_sims], each slice row-stochastic. NULL (default) builds an identity matrix per year and simulation. For observed bins that are a subset of the model ages, supply a shifted identity such as diag(1, n_model_ages)[, obs_age_index] instead.

AgeingError_fish_input

Optional per-fleet ageing error for the fishery fleets, [n_yrs × n_ages × n_obs_ages × n_fish_fleets × n_sims], or NULL (default) to read AgeingError_input.

AgeingError_srv_input

As AgeingError_fish_input with n_srv_fleets in place of n_fish_fleets.

LenBinMap_input

Matrix [n_lens × n_obs_lens] mapping the model's length bins onto the bins the length compositions are recorded on, the LenBinMap of Setup_Mod_Biologicals. NULL (default) when the two coincide.

CAAL_LenBinMap_input

0/1 matrix [n_lens × n_caal_lens] of the model length bins each conditional age-at-length row covers, the CAAL_LenBinMap of Setup_Mod_Biologicals. NULL (default) gives one row per model bin.

SizeAgeTrans_input

Size-age transition array [n_pop × n_regions × n_yrs × n_seas × n_lens × n_ages × n_sexes × n_sims], column-stochastic over ages. Only needed when fitting length compositions. Default NULL.

SizeAgeTrans_fish_input, SizeAgeTrans_srv_input

Optional per-fleet size-age arrays [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 and used in place of SizeAgeTrans_input. The self-test passes the fitted model's own keys here when growth was estimated.

Value

sim_list with $natmort, $WAA, $WAA_fish, $WAA_srv, $MatAA, $AgeingError (an identity matrix when none was supplied) and, when supplied, $LenBinMap and $SizeAgeTrans.

See also

Other Simulation Setup: Setup_Sim_Containers(), Setup_Sim_Dim(), Setup_Sim_Fishing(), Setup_Sim_Fleet_Devs(), 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()