Do Population Projections

Projects population dynamics forward in time under alternative recruitment and fishing mortality scenarios. The model initializes from terminal assessment quantities and advances numbers-at-age through recruitment, seasonal movement, mortality, ageing, and harvest control rules across multiple seasons and years.

Usage

Do_Population_Projection(
  n_proj_yrs = 2,
  n_pop,
  n_regions,
  n_ages,
  n_sexes,
  sexratio,
  n_fish_fleets,
  do_recruits_move = 0,
  recruitment,
  terminal_NAA,
  terminal_NAA0,
  terminal_F,
  dmr = array(0, dim = c(n_regions, n_seas, n_fish_fleets)),
  natmort,
  natal_region,
  WAA,
  WAA_fish,
  MatAA,
  fish_sel,
  ret_sel = array(1, dim = c(n_pop, n_regions, n_proj_yrs, n_seas, n_ages, n_sexes,
    n_fish_fleets)),
  Movement,
  sgl_seas_spawning_movement,
  stray_rate,
  f_ref_pt = NULL,
  b_ref_pt = NULL,
  HCR_function = NULL,
  recruitment_opt = "inv_gauss",
  fmort_opt = "HCR",
  t_spawn,
  bh_rec_opt = NULL,
  n_seas = 1,
  seasdur = rep(1/n_seas, n_seas),
  spawn_seas = 1,
  rec_seas_prop = {
     rec_seas_prop = array(0, dim = c(n_pop, n_seas))
    
rec_seas_prop[] <- 1/n_seas
     rec_seas_prop
 }
)

Arguments

n_proj_yrs

Integer. Number of projection years.

n_pop

Integer. Number of populations (may exceed regions when natal homing is modeled).

n_regions

Integer. Number of spatial regions.

n_ages

Integer. Number of age classes including the plus group.

n_sexes

Integer. Number of sexes.

sexratio

Array `[n_pop, n_regions, n_proj_yrs, n_sexes]`. Recruitment sex ratio used to allocate projected recruits by sex.

n_fish_fleets

Integer. Number of fishing fleets.

do_recruits_move

Integer (0 or 1). Whether age-1 recruits are subject to movement. Default = 0.

recruitment

Array `[n_pop, n_regions, n_yrs]`. Historical recruitment used to condition stochastic projection options.

terminal_NAA

Array `[n_pop, n_regions, n_seas, n_ages, n_sexes]`. Fished numbers-at-age in the terminal assessment year.

terminal_NAA0

Array `[n_pop, n_regions, n_seas, n_ages, n_sexes]`. Unfished numbers-at-age in the terminal assessment year.

terminal_F

Array `[n_regions, n_seas, n_fish_fleets]`. Terminal fishing mortality; sets F in projection year 1 and defines the seasonal F ratios applied in subsequent years.

dmr

Array [n_regions, n_seas, n_fish_fleets]. Discard mortality rate. Default behavior is no discard mortality (dmr = 0). When combined with ret_sel = 1, this implies no discarding within a given fleet (all catch is retained).

natmort

Array `[n_pop, n_regions, n_proj_yrs, n_ages, n_sexes]`. Annual natural mortality-at-age, scaled internally by season duration.

natal_region

Integer vector `[n_pop]`. Natal region for each population.

WAA

Array `[n_pop, n_regions, n_proj_yrs, n_seas, n_ages, n_sexes]`. Weight-at-age used in spawning biomass calculations.

WAA_fish

Array `[n_pop, n_regions, n_proj_yrs, n_seas, n_ages, n_sexes, n_fish_fleets]`. Fishery weight-at-age used in catch biomass calculations.

MatAA

Array `[n_pop, n_regions, n_proj_yrs, n_seas, n_ages, n_sexes]`. Maturity-at-age.

fish_sel

Array `[n_pop, n_regions, n_proj_yrs, n_seas, n_ages, n_sexes, n_fish_fleets]`. Fishery selectivity-at-age.

ret_sel

Array [n_pop, n_regions, n_proj_yrs, n_seas, n_ages, n_sexes, n_fish_fleets]. Retention selectivity-at-age. Default behavior corresponds to full retention (ret_sel = 1), meaning all captured fish are retained unless otherwise specified.

Movement

Array `[n_pop, n_regions, n_regions, n_proj_yrs, n_seas, n_ages, n_sexes]`. Seasonal movement transition matrices.

sgl_seas_spawning_movement

Array `[n_pop, n_regions, n_regions, n_proj_yrs, n_ages, n_sexes]`. Spawning movement matrix applied when `n_seas = 1` and `n_pop > 1` to redistribute fish to natal grounds prior to SSB calculation.

stray_rate

Array `[n_pop, n_proj_yrs]`. Per-population stray rate used when accumulating effective SSB contributions across populations.

f_ref_pt

Array `[n_regions, n_proj_yrs]`. Fishing mortality reference point (e.g., F_MSY) or fixed input F, depending on `fmort_opt`.

b_ref_pt

Array `[n_pop, n_regions, n_proj_yrs]`. Biomass reference point used in harvest control rules.

HCR_function

Function. Harvest control rule with arguments `x` (SSB), `frp` (F reference point), and `brp` (B reference point).

recruitment_opt

Character. Recruitment scenario: `"inv_gauss"`, `"mean_rec"`, `"zero"`, or `"bh_rec"`.

fmort_opt

Character. Fishing mortality scenario: `"HCR"`, `"HCR_global"`, or `"Input"`.

t_spawn

Numeric scalar. Fraction of the spawning season elapsed before spawning; used for mid-season SSB calculations.

bh_rec_opt

Named list of inputs for deterministic Beverton–Holt recruitment when `recruitment_opt = "bh_rec"`. This list is passed directly to Get_Det_Recruitment and must contain all required arguments for that function.

Required elements and their expected dimensions include:

R0: Numeric vector [n_pop]. Unfished recruitment.
h: Numeric array [n_pop, n_regions]. Steepness.
rec_region_prop: Numeric array [n_pop, n_regions]. Recruitment allocation across regions (sums to 1 across regions).
rec_seas_prop: Numeric array [n_pop, n_seas]. Seasonal recruitment proportions (sums to 1 across seasons).
SSB: Numeric array [n_pop, n_regions, n_yrs]. Historical spawning biomass, to which projected SSB is appended internally.
WAA: Array [n_pop, n_regions, n_seas, n_ages]. Weight-at-age.
MatAA: Array [n_pop, n_regions, n_seas, n_ages]. Maturity-at-age.
natmort: Array [n_pop, n_regions, n_ages]. Natural mortality.
Movement: Array [n_pop, n_regions, n_regions, n_seas, n_ages]. Movement transition matrices.
sgl_seas_spawning_movement: Array [n_pop, n_regions, n_regions, n_ages]. Spawning movement (single-season case).
stray_rate: Numeric vector [n_pop]. Straying rates.
init_F: Array [n_regions, n_seas, n_fish_fleets]. Initial fishing mortality.
fish_sel: Array [n_pop, n_regions, n_seas, n_ages, n_fish_fleets]. Total selectivity.
ret_sel: Array [n_pop, n_regions, n_seas, n_ages, n_fish_fleets]. Retention selectivity.
dmr: Array [n_regions, n_seas, n_fish_fleets]. Discard mortality rates.
sex_ratio_f: Numeric array [n_pop, n_regions]. Female recruitment proportion.

Additional scalar inputs include rec_dd, rec_lag, n_pop, n_regions, n_ages, n_seas, spawn_seas, seasdur, t_spawn, and do_recruits_move.

Spawning biomass used in recruitment is constructed internally by combining bh_rec_opt$SSB with projected SSB values during the simulation.

bh_rec_opt$rec_lag = 1 is the classic lagged case: each projection year's recruitment is computed up front from the prior year's SSB, exactly as recruitment_opt = "inv_gauss"/ "mean_rec" are. bh_rec_opt$rec_lag = 0 is age-0 recruitment: recruitment for year y is computed from year y's own SSB once spawn_seas is reached within that year's season loop, and is inserted no earlier than spawn_seas (rec_seas_prop must be zero for every season before spawn_seas in that case). Reference points and the seasonal SBPR calculation used to get bh_rec_opt$WAA/MatAA/etc. are unaffected by this choice – rec_lag only changes which year's SSB feeds the Beverton-Holt curve, not the per-recruit math itself.

n_seas

Integer. Number of seasons. Default = 1.

seasdur

Numeric vector `[n_seas]`. Duration of each season as a fraction of the year.

spawn_seas

Integer. Spawning season index.

rec_seas_prop

Array `[n_pop, n_seas]`. Proportion of annual recruitment entering in each season. Must sum to 1 across seasons for each population.

Value

A named list containing projected fishing mortality, catch, spawning biomass, effective spawning biomass, dynamic unfished biomass, and numbers-at-age for fished and unfished states.

Details

Population dynamics are tracked at full resolution over [population x region x year x season x age x sex]. Recruitment is generated annually and then distributed across seasons using rec_seas_prop, allowing intra-annual timing of recruitment within the first age class.

Each projection year proceeds as follows when recruitment_opt != "bh_rec" or bh_rec_opt$rec_lag != 0 (the classic case):

Annual recruitment is generated and allocated across regions and sexes. Seasonal recruitment is then distributed within the first age class using rec_seas_prop, with additional recruits entering in seasons seas > 1.
Fishing mortality-at-age is constructed from annual F, seasonal F ratios derived from the terminal year, and selectivity.
Movement is applied at each seasonal step via transition matrices. Age-1 movement is optional via do_recruits_move.
Within-season mortality is applied using exponential decay. At the end of the final season, individuals age forward and the plus group accumulates survivors.
Spawning biomass is computed in spawn_seas using a mid-season mortality correction. For natal homing models with a single season, spawning movement is applied prior to SSB calculation.
Catch is calculated using the Baranov equation and aggregated to biomass using fishery-specific weights.
Fishing mortality for the next year is updated via the specified harvest control rule or fixed input.

When bh_rec_opt$rec_lag == 0 (age-0 recruitment), steps 1 and 5 above are reordered within spawn_seas: movement is applied first, spawning biomass is computed from the survivor population alone (no new recruits exist yet), that SSB is used to generate this year's recruitment, and only then are the recruits inserted (no earlier than spawn_seas) - immediately before mortality/ageing runs for that season, so the new cohort is carried forward exactly like any other seasonal recruit pulse. Years y > 1 generate recruitment this way; year 1 carries the supplied terminal assessment state forward with no new recruitment event, matching the classic case.

Effective spawning biomass at each population's natal region aggregates contributions from all populations, with cross-population contributions scaled by stray_rate and normalised by the number of populations in each natal region.

When n_sexes = 1, spawning biomass is multiplied by 0.5. When n_regions = 1, movement is skipped.

Usage

Arguments

Value

Details

See also