Population dynamics — do

Runs the core age- and season-structured population dynamics loop for southern bluefin tuna. The loop applies catch-conditioned removals, natural mortality, spawning, and Beverton-Holt recruitment with lognormal deviations. Standard fisheries use selectivity-based catch conditioning; optional direct-removal fisheries use sliced age frequencies.

Usage

do_dynamics(
  first_yr,
  first_yr_catch,
  B0 = 6400000,
  R0,
  alpha,
  beta,
  h = 0.7,
  sigma_r = 0.6,
  rdev_y,
  M_a,
  phi_ya,
  init_number_a,
  removal_switch_f,
  catch_obs_ysf,
  sel_fya,
  weight_fya,
  af_sliced_ysfa,
  harvest_wall = NULL,
  report = FALSE
)

Arguments

first_yr: Integer first model year (e.g., 1931).
first_yr_catch: Integer first year with catch data, which determines when fishing begins.
B0: Numeric unfished equilibrium spawning biomass.
R0: Numeric unfished equilibrium recruitment.
alpha: Numeric Beverton-Holt stock-recruitment alpha parameter.
beta: Numeric Beverton-Holt stock-recruitment beta parameter.
h: Numeric steepness parameter retained for interface compatibility. The supplied alpha and beta already encode steepness, so this argument is not read by the dynamics loop.
sigma_r: Numeric standard deviation of log recruitment deviations.
rdev_y: Vector of log recruitment deviations, one per modeled recruitment year.
M_a: Vector of natural mortality rates indexed by age.
phi_ya: Matrix of spawning output per fish at age, with dimensions (n_year + 1) by n_age, created by get_phi().
init_number_a: Vector of initial numbers-at-age for year 1, season 1.
removal_switch_f: Integer vector of length n_fishery: 0 uses catch-conditioned selectivity and 1 uses direct sliced age frequencies.
catch_obs_ysf: A 3D array of observed catch weights with dimensions catch year by season by fishery.
sel_fya: A 3D array of fishery selectivity-at-age with dimensions fishery by year by age, created by get_selectivity().
weight_fya: A 3D array of mean weight-at-age in tonnes per fish, with dimensions n_fishery by n_year by n_age.
af_sliced_ysfa: A 4D array of sliced age-frequency numbers with dimensions year by season by fishery by age. It is used only for fisheries whose removal switch is 1.
harvest_wall: Optional named list with strength, onset, ceiling, and scale. These values are passed to harvest_wall_contract() inside the dynamics. NULL uses the disabled contract and is intended for direct diagnostic or projection calls; sbt_model() always supplies the explicit settings prepared by get_data().
report: Logical. If TRUE, register dynamics and penalty outputs with RTMB::REPORT(). The assessment objective sets this to true; direct calls default to no reporting side effects.

Value

A list containing:

number_ysa: Updated numbers-at-age by year, season, and age.
spawning_biomass_y: Spawning biomass by year.
recruitment_y: Recruitment by year.
hrate_ysfa: Raw fishery-specific harvest rates.
hrate_raw_ysa,hrate_ysa: Raw total and positive-continuation harvest rates used by the dynamics.
survival_raw_ysa,survival_used_ysa: Raw and continued survival after fishing.
harvest_penalty_ysa,harvest_penalty_ys: Age-specific and aggregated feasibility penalties.
catch_pred_fya: Predicted catch numbers by fishery, year, and age.
catch_pred_ysf: Predicted catch weights by year, season, and fishery.
harvest_wall_penalty_ysa: Preventive-wall contribution by cell.
lp_feasibility: Total positive-survival continuation penalty.
lp_harvest_wall: Total preventive harvest-wall penalty.
lp_penalty: Sum of lp_feasibility and lp_harvest_wall.

Details

The implementation is specialized to the assessment's two seasons and six fisheries. It preserves each observed total catch exactly when constructing removals. The smooth positive continuation is an objective feasibility device and does not replace the separate biological-state acceptance checks.