Population dynamics — do

Runs the core age- and season-structured population dynamics loop for Southern Bluefin Tuna. Starts from initial equilibrium numbers (derived from B0 and h), applies seasonal harvest, natural mortality, spawning, recruitment (Beverton-Holt + log-normal deviates), and computes predicted catches and harvest rates. Handles both standard Baranov harvest (removal_switch_f == 0) and direct age-sliced removals (removal_switch_f == 1).

Usage

do_dynamics(
  first_yr,
  first_yr_catch,
  B0,
  R0,
  alpha,
  beta,
  h,
  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
)

Arguments

first_yr: Integer first model year (e.g., 1931).
first_yr_catch: Integer first year with catch data (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 (0.2-1.0) of the Beverton-Holt stock-recruitment relationship.
sigma_r: Numeric standard deviation of log recruitment deviations (default = 0.6).
rdev_y: A vector of log-scale recruitment deviations of length n_year (one per recruitment year).
M_a: A vector of natural mortality rates indexed by age (length n_age).
phi_ya: A matrix of spawning output (maturity × fecundity × weight) per recruit at age with dimensions (n_year + 1) by n_age (pre-computed via get_phi).
init_number_a: A vector of initial numbers-at-age (length n_age) for year 1, season 1.
removal_switch_f: An integer vector of length n_fishery indicating removal type: 0 = standard Baranov harvest rate, 1 = direct removal using sliced age frequencies.
catch_obs_ysf: A 3D array of observed catch weights with dimensions n_catch_years by n_season by n_fishery.
sel_fya: A 3D array of fishery-specific selectivity-at-age with dimensions n_fishery by n_year by n_age (pre-computed via get_selectivity).
weight_fya: A 3D array of mean weight-at-age with dimensions n_fishery by n_year by n_age.
af_sliced_ysfa: A 4D array of sliced age-frequency numbers with dimensions n_year by n_season by n_fishery by n_age (used only when removal_switch_f == 1).

Value

A list containing:

number_ysa: 3D array of updated numbers-at-age with dimensions (n_year + 1) by n_season by n_age.
spawning_biomass_y: Vector of spawning biomass by year (length n_year + 1).
hrate_ysfa: 4D array of harvest rates with dimensions (n_year + 1) by n_season by n_fishery by n_age.
hrate_ysa: 3D array of total harvest rates with dimensions (n_year + 1) by n_season by n_age.
catch_pred_fya: 3D array of predicted catch numbers with dimensions n_fishery by (n_year + 1) by n_age.
catch_pred_ysf: 3D array of predicted catch weights with dimensions (n_year + 1) by n_season by n_fishery.
lp_penalty: Numeric total penalty from posfun (harvest rate constraints).