Set up recruitment dynamics for the operating model simulation

Sets the stock-recruit form and density dependence, $R_0$, steepness, sex ratio, the recruitment and initial age deviations, seasonal allocation, spawn timing and the equilibrium initialization. Call after Setup_Sim_Dim.

Usage

Setup_Sim_Rec(
  sim_list,
  do_recruits_move = 0,
  sexratio_input = array(if (sim_list$n_sexes == 1) 1 else 0.5, dim = c(sim_list$n_pop,
    sim_list$n_regions, sim_list$n_yrs, sim_list$n_sexes, sim_list$n_sims)),
  R0_input = array(15, dim = c(sim_list$n_pop, sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_sims)),
  rinit_input = array(15, dim = c(sim_list$n_pop, sim_list$n_regions, sim_list$n_sims)),
  h_input = array(0.8, dim = c(sim_list$n_pop, sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_sims)),
  stray_rate_input = array(0, dim = c(sim_list$n_pop, sim_list$n_yrs, sim_list$n_sims)),
  ln_sigmaR = array(log(1), dim = c(2, sim_list$n_pop, sim_list$n_regions)),
  rec_seas_prop_input = {
     rec_seas_prop = array(0, dim = c(sim_list$n_pop,
    sim_list$n_seas, sim_list$n_sims))
rec_seas_prop[, 1, ] <- 1
     rec_seas_prop

    },
  recruitment_opt = "bh_rec",
  rec_dd = "global",
  init_dd = "global",
  use_rinit = 0,
  init_age_strc = 2,
  spawn_seas = 1,
  t_spawn = 0,
  rec_lag = 1,
  SR_ref_yr = 1,
  Rec_input = NULL,
  ln_InitDevs_input = NULL,
  ln_RecDevs_input = NULL,
  InitDevs_sex_spec = "est_shared_s",
  RecDevs_model = "iid",
  RecDevs_rho = array(0, dim = c(sim_list$n_pop, sim_list$n_regions)),
  sigmaR_switch = 1
)

Arguments

sim_list: Simulation list returned by Setup_Sim_Dim.
do_recruits_move: Integer flag. 0 (default) starts movement at age 2, 1 moves recruits from age 1.
sexratio_input: Proportion of recruits per sex, array [n_pop x n_regions x n_yrs x n_sexes x n_sims]. Default 1 for one sex, 0.5 each for two.
R0_input: Unfished equilibrium recruitment array [n_pop x n_regions x n_yrs x n_sims]. Default 15.
rinit_input: Equilibrium recruitment used for initialization under use_rinit = 1, array [n_pop x n_regions x n_sims]. Default 15.
h_input: Steepness array [n_pop x n_regions x n_yrs x n_sims], values in $(0.2, 1)$. Default 0.8.
stray_rate_input: Natal-homing stray rate array [n_pop x n_yrs x n_sims], the proportion straying from the natal region at spawning. Default 0.
ln_sigmaR: Log-scale sd of the recruitment deviations, array [2 x n_pop x n_regions], index 1 the early period and 2 the late period. The initial age deviations read index 1. Default log(1). A later Setup_Sim_DSEM that links recruitment overwrites both indices with that series' settled value under the arrows, the same number the fit's own penalty reads. A series that never settles falls back a step: a walk reads its own sd line, and a moderated variance, having no sd line, leaves what is passed here standing.
rec_seas_prop_input: Seasonal allocation of annual recruitment, array [n_pop x n_seas x n_sims] summing to 1 across seasons. Default all in season 1. Must be zero before spawn_seas when rec_lag = 0 and spawn_seas > 1.
recruitment_opt: Recruitment model, default "bh_rec". 0/"mean_rec" has no stock-recruit relationship, 1/"bh_rec" is Beverton-Holt and requires rec_dd = "local" when n_pop > 1, and 999/"resample_from_input" resamples years from Rec_input, using historical years as they are and sampling projection years with replacement so spatial covariance within a year is kept.
rec_dd: Density dependence for the stock-recruit relationship, default "global". 0/"local" gives each region its own $R_0$ and steepness, required when n_pop > 1 under "bh_rec"; 1/"global" pools across regions.
init_dd: Density dependence for equilibrium initialization, same options as rec_dd. Default "global".
use_rinit: Integer (0/1). Whether rinit_input initializes the population separately from R0_input. Under 0 (default) rinit_input is ignored.
init_age_strc: Equilibrium initialization method, default 2. 0/"iterative" iterates forward to approximate equilibrium, 1/"scalar_no_move" is a scalar geometric series without movement, 2/"matrix" is the matrix series with movement, and 3/"scalar_plus_only" moves only the plus group. 4/"free" projects no equilibrium: ln_InitDevs are the initial log numbers-at-age for ages 2 and above, apportioned by sex ratio, so the initial condition ignores init_F_par and ln_rinit and any penalty becomes a prior on initial abundance.
spawn_seas: Integer index of the spawning season. Default 1.
t_spawn: Spawn timing as a fraction of spawn_seas elapsed before spawning. 0 (default) spawns before any mortality, 1 after all of it.
rec_lag: Integer seasons between spawning and recruitment. 1 (default) uses SSB from that many seasons prior, in any season. 0 is age-0 recruitment on the same year's SSB, so recruits may only enter in spawn_seas or later and rec_seas_prop_input must be zero before it.
SR_ref_yr: Integer year index supplying the biological inputs to unfished spawning biomass per recruit, and so the curve's scale. Matches the estimation model's SR_ref_yr. Default 1.
Rec_input: External recruitment array [n_pop x n_regions x n_yrs x n_sims], required under recruitment_opt = "resample_from_input". Projection years beyond its length are resampled from historical years with replacement. Default NULL.
ln_InitDevs_input: Optional log-scale initial age deviations, either [n_pop x n_regions x (n_ages - 1) x n_sims] for one shared curve or [n_pop x n_regions x (n_ages - 1) x n_sexes x n_sims] for one per sex. The n_ages - 1 dim excludes the reference age. NULL (default) draws one shared curve per population and region; pass zeros to start in equilibrium.
ln_RecDevs_input: Optional log recruitment deviations [n_pop x n_regions x n_input_yrs x n_sims], used as given in every year they cover instead of being drawn, the years after them drawn as usual. A year that Rec_input covers takes its recruitment from there. Default NULL.
InitDevs_sex_spec: How initial age deviations are drawn across sexes when ln_InitDevs_input is not supplied. "est_shared_s" (default) draws one curve per population or region for every sex, "est_all" draws each sex its own. Names match Setup_Mod_Rec.
RecDevs_model: Process error the deviations are drawn under. "iid" (default) is independent, "rw" a random walk, "ar1" reverts toward zero at rate RecDevs_rho. Year one is drawn at ln_sigmaR under the first two and from ln_sigmaR / sqrt(1 - RecDevs_rho^2) under "ar1". Matches Setup_Mod_Rec.
RecDevs_rho: Matrix [n_pop x n_regions] of AR1 correlations in $(-1, 1)$. Only read under RecDevs_model = "ar1". Default zero.
sigmaR_switch: Integer year index at which the recruitment deviations switch from index 1 of ln_sigmaR to index 2, matching Setup_Mod_Rec. Default 1, which reads index 2 in every year.

Value

sim_list with $recruitment_opt, $rec_dd, $init_dd, $R0, $h, $sexratio, $ln_sigmaR, $rec_seas_prop, $spawn_seas, $t_spawn, $rec_lag, $init_age_strc, $do_recruits_move, $move_age, $stray_rate, and optionally $Rec_input, $ln_InitDevs_input and $ln_RecDevs_input. Character codes are converted to integers before storage.

Set up recruitment dynamics for the operating model simulation

Usage

Arguments

Value

See also