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Specify the state-space numbers-at-age process for simulation

Setup_Sim_NAA_state.Rd

Turns on process error in the numbers at age for a simulated population. The operating model applies the same centered state the estimation model does: the deterministic mortality and ageing step is computed, then the numbers are multiplied by \(\exp(\eta)\) with \(\eta\) drawn from the covariance the arguments here describe.

Usage

Setup_Sim_NAA_state(
  sim_list,
  NAA_re = "none",
  sigmaNAA = 0.3,
  rho_age = 0,
  rho_year = 0,
  rho_cohort = 0,
  NAA_re_pop = "iid",
  NAA_re_region = "iid",
  NAA_re_sex = "iid",
  NAA_re_season = "iid",
  pop_corr = 0,
  region_corr = 0,
  sex_corr = 0,
  season_corr = 0,
  NAA_re_ages = NULL,
  NAA_re_years = NULL,
  NAA_re_seasons = "annual"
)

Arguments

sim_list

Simulation list from Setup_Sim_Dim.

NAA_re

Character. "none" (default) leaves the numbers at age deterministic past recruitment and the initial age structure. Otherwise one of "iid", "1dar1_a", "1dar1_y", "2dar1", "3dcond" or "3dmarg".

sigmaNAA

Numeric. Conditional standard deviation of the innovations, the same quantity ln_sigmaNAA holds in the estimation model. Under an autoregressive form the marginal standard deviation is larger by \(1/\sqrt{1 - \rho^2}\) per correlated dim.

rho_age, rho_year, rho_cohort

Numeric correlations in \((-1, 1)\) over the age, year and cohort dims. Only the ones the chosen form reads are used.

NAA_re_pop, NAA_re_region, NAA_re_sex, NAA_re_season

Character, "iid" (default) or "us", an unstructured correlation across that dim.

pop_corr, region_corr, sex_corr, season_corr

Numeric vectors of length \(n(n-1)/2\) giving the correlations for those dims, ordered as the strict lower triangle is filled by column. A single value is recycled.

NAA_re_ages, NAA_re_years

Ages and year indices the state covers. NULL (default) uses everything from the second onward.

NAA_re_seasons

Seasons the state covers. "annual" (default) puts a state at season one only, leaving the numbers deterministic between seasons; "all" puts one at the start of every season, and an integer vector selects specific seasons.

Value

sim_list with the state-space settings attached.

Details

Arguments mirror Setup_Mod_Biologicals's state-space options so a simulated population and the model fitted to it are written the same way, which is what makes a self test a like-for-like comparison rather than a translation.

See also

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