Set up recruitment dynamics for the operating model simulation

Populates sim_list with all recruitment-related inputs needed by the operating model: stock-recruit relationship type and density-dependence structure, biological parameters ($R_0$, steepness, sex ratio), recruitment and initial age-structure deviations, seasonal recruitment allocation, spawn timing, and equilibrium initialisation method. Must be called 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,
  Rec_input = NULL,
  ln_InitDevs_input = NULL
)

Arguments

sim_list

Simulation list returned by Setup_Sim_Dim.

do_recruits_move

Integer flag. 0 = age-1 fish do not move (default); movement begins at age 2. 1 = recruits participate in movement from age 1.

sexratio_input

Proportion of recruits assigned to each sex, array [n_pop x n_regions x n_yrs x n_sexes x n_sims]. Default: 1 when n_sexes = 1; 0.5 per sex when n_sexes = 2.

R0_input

Unfished equilibrium recruitment array [n_pop x n_regions x n_yrs x n_sims]. Default: 15 for all cells.

rinit_input

Unfished equilibrium recruitment scalar used for population initialisation when use_rinit = 1, array [n_pop x n_regions x n_sims]. Ignored when use_rinit = 0. Default: 15 for all cells.

h_input

Beverton-Holt steepness array [n_pop x n_regions x n_yrs x n_sims]. Values should be in $(0.2, 1)$. Default: 0.8.

stray_rate_input

Natal-homing stray rate array [n_pop x n_yrs x n_sims]. Proportion of individuals that stray from their natal region during spawning. Default: 0 (No individuals stray).

ln_sigmaR

Log-scale standard deviation of recruitment deviations, array [2 x n_pop x n_regions]. The first element controls the SD for initial age-structure deviations (ln_InitDevs); the second controls the SD for annual recruitment deviations (ln_RecDevs). Default: log(1) for both.

rec_seas_prop_input

Seasonal allocation of annual recruitment, array [n_pop x n_seas x n_sims]. Each population's values should sum to 1 across seasons. Default: all recruitment assigned to season 1. When rec_lag = 0 and spawn_seas > 1, must be zero for every season before spawn_seas – an error is raised otherwise.

recruitment_opt

Recruitment model. Default "bh_rec". Options:

0/"mean_rec": Mean recruitment; no stock-recruit relationship.
1/"bh_rec": Beverton-Holt stock-recruit relationship. Requires rec_dd = "local" when n_pop > 1.
999/"resample_from_input": Bootstrap recruitment by resampling years from Rec_input. Historical years are used as-is; projection years are sampled with replacement, preserving spatial covariance among regions within each resampled year. Requires Rec_input to be non-NULL.

rec_dd

Density-dependence structure for the stock-recruit relationship. Default "global". Options:

0/"local": Region-specific spawner-recruit relationship; each region has its own $R_0$ and steepness. Required when n_pop > 1 and recruitment_opt = "bh_rec".
1/"global": Single shared spawner-recruit relationship pooled across regions.

init_dd

Density-dependence structure for equilibrium age-structure initialisation. Default "global". Same options as rec_dd.

use_rinit

Integer (0/1). Whether a separate initial recruitment scalar rinit_input is used to initialise the population independently of R0_input. When 0 (default), rinit_input is ignored and R0_input governs both initialisation and recruitment. When 1, rinit_input is used exclusively for equilibrium initialisation and R0_input governs the recruitment relationship.

init_age_strc

Integer specifying the equilibrium age-structure initialisation method. Default 2. Options:

0/"iterative": Iterates the population forward until approximate equilibrium. Slowest but most general.
1/"scalar_no_move": Scalar geometric series solution assuming no movement in any age class.
2/"matrix": Matrix geometric series solution that generalises the scalar approach to include movement. Recommended default for spatially explicit models.
3/"scalar_plus_only": Scalar geometric series solution assuming no movement except in the plus group.

spawn_seas

Integer index of the season in which spawning occurs. Default 1.

t_spawn

Spawn timing as a fraction of the season elapsed before spawning within spawn_seas. 0 (default) = spawning occurs before any mortality is applied in that season; 1 = spawning occurs after all mortality.

rec_lag

Integer. Number of seasons between spawning and recruitment. 1 (default) is the classic lagged case: recruits enter the population using SSB from rec_lag seasons prior, in any season. 0 is age-0 recruitment: recruits enter using the SAME year's SSB. Because that SSB isn't known until spawn_seas is reached, age-0 recruits may only enter in spawn_seas itself or a later season in the same year – rec_seas_prop_input must be zero for every season before spawn_seas when rec_lag = 0.

Rec_input

External recruitment array [n_pop x n_regions x n_yrs x n_sims]. Required when recruitment_opt = "resample_from_input"; projection years beyond the length of Rec_input are filled by resampling historical years with replacement. Ignored for other recruitment options. Default NULL.

ln_InitDevs_input

Optional log-scale initial age-structure deviations array [n_pop x n_regions x (n_ages - 1) x n_sims]. The n_ages - 1 dimension excludes the reference age used during initialisation. If NULL (default), deviations are initialised to zero.

Value

The input sim_list with recruitment-related fields appended: $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 and $ln_InitDevs_input. Character-coded inputs are converted to their integer equivalents before storage.

Set up recruitment dynamics for the operating model simulation

Usage

Arguments

Value

See also