Skip to contents

Initialize simulation dimension settings

Source: R/setup_dimensions.R
Setup_Sim_Dim.Rd

Creates the foundational sim_list object used throughout a closed-loop simulation or static simulation. All downstream setup functions (Setup_Sim_Biologicals, Setup_Sim_Containers, etc.) expect a sim_list produced by this function. Dimension scalars are validated on input and stored alongside derived quantities such as init_iter and the natal_region mapping.

Usage

Setup_Sim_Dim(
  n_sims,
  n_yrs,
  n_pop = 1,
  n_seas = 1,
  n_regions,
  natal_region = NULL,
  n_ages,
  n_lens = NULL,
  n_obs_ages = n_ages,
  n_obs_lens = n_lens,
  n_caal_lens = n_lens,
  n_sexes,
  n_fish_fleets,
  n_srv_fleets,
  seasdur = if (n_seas == 1) 1 else rep(1/n_seas, n_seas),
  run_feedback = FALSE,
  feedback_start_yr = NULL,
  bias_correct_pe = "rec",
  bias_correct_oe = 0
)

Arguments

n_sims

Positive integer. Number of simulation replicates.

n_yrs

Positive integer. Number of projection years.

n_pop

Positive integer. Number of distinct populations (default 1). Populations share movement and selectivity schedules but can have independent stock-recruit relationships and natal regions.

n_seas

Positive integer. Number of seasons within each year (default 1).

n_regions

Positive integer. Number of spatial regions.

natal_region

Integer vector of length n_pop mapping each population to its natal region (1-indexed). Defaults are applied when NULL:

  • n_regions == 1: all populations assigned to region 1.

  • n_pop == n_regions: one-to-one mapping (1:n_pop).

  • n_pop == 1: assigned to region 1.

Must be supplied explicitly when n_pop > 1, n_pop != n_regions, and n_regions > 1, as multiple populations would share a natal region and no sensible default exists.

n_ages

Positive integer. Number of modeled age classes.

n_lens

Positive integer. Number of length bins. Set to NULL (default) when length compositions are not simulated.

n_obs_ages

Positive integer. Number of observed age bins in composition and at-age data, the columns of AgeingError_input. Can differ from n_ages when the plus group or youngest ages are pooled differently in observations. Defaults to n_ages.

n_obs_lens

Positive integer. Number of length bins the length compositions are recorded on, the columns of LenBinMap_input in Setup_Sim_Biologicals. Defaults to n_lens.

n_caal_lens

Positive integer. Number of length rows of the conditional age-at-length data, the columns of CAAL_LenBinMap_input in Setup_Sim_Biologicals. Defaults to n_lens.

n_sexes

Integer. Number of sexes; must be either 1 (sex-aggregated) or 2 (sex-structured).

n_fish_fleets

Positive integer. Number of fishery fleets.

n_srv_fleets

Positive integer. Number of survey fleets.

seasdur

Numeric vector of length n_seas giving the duration of each season as a fraction of a year. Values must sum to 1. Defaults to 1 when n_seas == 1, or rep(1 / n_seas, n_seas) for equal-length seasons otherwise.

run_feedback

Logical. Whether to run a closed-loop feedback MSE in which an estimation model and harvest control rule update fishing mortality each year. Default FALSE (open-loop simulation).

feedback_start_yr

Integer. First year in which feedback is applied. Required when run_feedback = TRUE; ignored otherwise.

bias_correct_pe

Which log scale process deviations the operating model centers on minus half their marginal variance: "none", "rec" (default, recruitment and the initial ages) or "all" (those plus the numbers at age state).

bias_correct_oe

Whether a lognormally simulated observation is drawn at its mean rather than its median, 0 (default, the median) or 1. Both switches are the same ones Setup_Mod_Dim takes, and a self test needs the same value on each side.

Value

A named list (sim_list) containing:

n_sims, n_yrs, n_pop, n_regions, n_seas, n_ages, n_obs_ages, n_lens, n_obs_lens, n_caal_lens, n_sexes, n_fish_fleets, n_srv_fleets

Dimension scalars supplied as inputs.

natal_region

Integer vector of length n_pop defining natal regions.

seasdur

Season durations summing to 1.

init_iter

Derived value n_ages * 10 used to initialize equilibrium conditions.

run_feedback, feedback_start_yr

Feedback control settings.

See also

Other Simulation Setup: Setup_Sim_Biologicals(), Setup_Sim_Containers(), 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()