Population projection (numbers-at-age dynamics) — get_population

Advances numbers at age through every modeled year and season: inserts recruitment at the timing rec_lag sets, applies movement, computes the biomass quantities through compute_biom_y, and applies mortality and ageing. ZAA is an input here, not derived from NAA, so it must already be computed. Called once from the population projection section of SPoRC_rtmb.R.

Usage

get_population_projection(
  n_pop,
  n_regions,
  n_seas,
  n_ages,
  n_sexes,
  n_yrs,
  n_fish_fleets,
  n_est_rec_devs,
  rec_lag,
  rec_model,
  rec_dd,
  R0,
  rec_region_prop,
  rec_seas_prop,
  h_trans,
  R0_yr = NULL,
  natal_region,
  t_spawn,
  spawn_seas,
  seasdur,
  init_F,
  ln_RecDevs,
  sexratio,
  WAA,
  MatAA,
  natmort,
  Movement,
  stray_rate,
  sgl_seas_spawning_movement,
  do_recruits_move,
  fish_sel,
  ret_sel,
  dmr,
  ZAA,
  NAA,
  NAA0,
  NAA_bef,
  NAA_aft,
  Rec,
  SSB,
  Total_Biom,
  Dynamic_SSB0,
  eff_SSB,
  Mrate = NULL,
  move_timing = 0,
  SR_ref_yr = 1,
  sr_penalty = 0,
  sr_R0 = NULL,
  growth_mortality_year_fn = NULL,
  growth_mortality_state = NULL,
  expm_nsub = 0,
  n_est_naa_re = 0,
  ln_NAA = NULL,
  naa_re_ages = NULL,
  naa_re_yrs = NULL,
  naa_re_seas = NULL
)

Arguments

n_pop, n_regions, n_seas, n_ages, n_sexes, n_yrs, n_fish_fleets: Dimension sizes.
n_est_rec_devs: Number of estimated recruitment deviations.
rec_lag: Integer. 0 inserts recruitment inside the spawning-season biomass computation; non-zero inserts it once a year ahead of the seasonal loop.
rec_model, rec_dd, R0, rec_region_prop, rec_seas_prop, h_trans, natal_region, t_spawn, spawn_seas, seasdur, init_F: Recruitment and timing arguments passed through to Get_Det_Recruitment.
R0_yr: Matrix [n_pop x n_yrs] of R0 by year when R0 has time blocks, or NULL for the single R0. Only the recruitment computed each year reads it; everything needing one value still uses R0.
ln_RecDevs: Array [pop, region, year] of log recruitment deviations, applied multiplicatively to deterministic recruitment for y <= n_est_rec_devs.
sexratio: Array [pop, region, year, sex] of the recruitment sex ratio.
WAA, MatAA, natmort: Arrays [pop, region, year, season, age, sex] of weight at age, maturity at age and natural mortality.
Movement: Array [pop, region_from, region_to, year, season, age, sex] of movement rates.
stray_rate: Array [pop, year] of stray rate.
sgl_seas_spawning_movement: Array [pop, region_from, region_to, year, age, sex] of single-season spawning movement.
do_recruits_move: Integer (0/1) for whether age-1 recruits move.
fish_sel, ret_sel: Arrays [pop, region, year, season, age, sex, fish_fleet] of total and retained fishery selectivity.
dmr: Array [region, year, season, fish_fleet] of discard mortality rate.
ZAA: Array [pop, region, year, season, age, sex] of total mortality at age, precomputed.
NAA, NAA0, NAA_bef, NAA_aft: Arrays [pop, region, year+1, season, age, sex], the output containers for the fished and unfished numbers at age and for the numbers immediately before and after movement.
Rec: Array [pop, region, year], the output container for total recruitment before seasonal apportionment.
SSB, Total_Biom, Dynamic_SSB0: Arrays [pop, region, year], output containers.
eff_SSB: Array [pop, year], the output container for effective (natal-homing-adjusted) SSB.
SR_ref_yr: Integer year index supplying the biological inputs (weight at age, maturity, natural mortality and movement) to unfished spawning biomass per recruit, and so to S0 and the curve's scale. Default 1. Set it to n_yrs to condition the curve on terminal weight at age, as several ADMB assessments do. It is an index, not a calendar year, so a caller that truncates the year dim must clamp it.
growth_mortality_year_fn: Optional function of (y, NAA_y, growth_mortality_state) called at the top of every year with the numbers at age at the start of that year, array [pop, region, age, sex], and the state kept from the previous year. It returns a list with state, advanced to the next call and returned to the caller, and ZAA_y, WAA_y and MatAA_y, which replace that year's slices. Passing the state in and out keeps the per-year step a function of its arguments.
growth_mortality_state: Initial state for growth_mortality_year_fn, passed through the year loop and returned. NULL (default) uses the arrays as given. This is how cohort growth, whose plus group blends by numbers, is evaluated inside the year loop.
n_est_naa_re: Number of estimated state-space numbers at age. Zero leaves the numbers deterministic. Never inferred from dim(ln_NAA), which is non-zero once the setup function has run at all.
ln_NAA: Array [pop, region, year, season, age, sex] of log numbers at the start of a season, overwriting the deterministic prediction wherever the state is active. Season one is the year boundary, after ageing and the plus group; later seasons are states on the within-year survival step.
naa_re_ages, naa_re_yrs, naa_re_seas: Integer index vectors the state is active over.

Value

List with NAA, NAA0, NAA_bef, NAA_aft, Rec, SSB, Total_Biom, Dynamic_SSB0, eff_SSB, Aggregated_SSB and Dynamic_Aggregated_SSB0 (arrays [year], summed across population and region), and NAA_int [pop, region, year, season, age, sex], the season-integrated abundance the spatial Baranov equation needs, populated only under move_timing = 2 and all zeros otherwise.

Details

Every array argument matching an output name is passed in already dimensioned, usually all zero aside from any initial-year values inserted upstream, and comes back filled over 1:n_yrs.