Compute fishing and biological reference points from an assessment or simulation

Wrapper that constructs the appropriate data list, calls the relevant inner objective function via RTMB, and returns fishing and biological reference points for use in projections or harvest control rules. Supports single-region and spatially explicit multi-region models, with options for SPR-based or Beverton-Holt MSY-based reference points.

Usage

Get_Reference_Points(
  data,
  rep,
  SPR_x = NULL,
  t_spawn = 0,
  sex_ratio_f = array(0.5, dim = c(data$n_pop, data$n_regions)),
  calc_rec_st_yr = 1,
  rec_age = 1,
  type,
  what,
  n_avg_yrs = 1,
  local_bh_msy_newton_steps = 6,
  is_discard_fleet = array(0, dim = data$n_fish_fleets)
)

Arguments

data

List. SPoRC data object containing age structure, weight-at-age, maturity, natural mortality, seasons, and spatial configuration.

rep

List. SPoRC report object from RTMB containing estimated or simulated quantities including Fmort, fish_sel, natmort, Rec, SSB, h_trans, R0, rec_region_prop, rec_seas_prop, Movement, and stray_rate.

SPR_x

Numeric. Target spawning potential ratio fraction (e.g. 0.4). Required when what is "SPR", "independent_SPR", or "global_SPR".

t_spawn

Numeric. Fraction of the spawning season elapsed before spawning, used for the mid-season mortality correction. Default = 0.

sex_ratio_f

Numeric array [n_pop, n_regions]. Female sex ratio at recruitment. Default = 0.5 everywhere.

calc_rec_st_yr

Integer. First year included when computing mean historical recruitment for biological reference point scaling. Default = 1.

rec_age

Integer. Recruitment lag in years, used to exclude the most recent years from the mean recruitment calculation. Default = 1.

type

Character. Spatial structure of the model:

"single_region": No spatial movement; supports "SPR" and "BH_MSY".
"multi_region": Spatially explicit; supports "independent_SPR", "independent_BH_MSY", "global_SPR", "global_BH_MSY", and "local_BH_MSY".

what

Character. Reference point method:

"SPR": Single-region \(F_{SPR_x}\).
"BH_MSY": Single-region Beverton-Holt \(F_{MSY}\).
"independent_SPR": Per-region \(F_{SPR_x}\) computed independently for each region without movement.
"independent_BH_MSY": Per-region \(F_{MSY}\) computed independently for each region without movement.
"global_SPR": Single shared \(F_{SPR_x}\) with movement, integrated across all regions.
"global_BH_MSY": Single shared \(F_{MSY}\) with movement. Valid for single-population models only.
"local_BH_MSY": Region-specific \(F_{MSY}\) values that jointly maximise total yield with movement. Valid for both single- and multi-population models.

n_avg_yrs

Integer. Number of terminal years over which demographic rates (selectivity, natural mortality, weight, maturity, movement) are averaged before computing reference points. Default = 1.

local_bh_msy_newton_steps

Integer. Number of Newton-Raphson iterations used to solve for equilibrium recruitment by origin region when what = "local_BH_MSY". Increase if convergence is suspect. Default = 6.

is_discard_fleet

Integer vector [n_fish_fleets]. Indicator for fleets whose catch should be excluded from landed yield when computing MSY-based reference points (0 = landing fleet, 1 = discard-only fleet). These fleets still contribute to total fishing mortality Z and affect population dynamics and spawning biomass. Only used by Beverton–Holt MSY methods ("BH_MSY", "independent_BH_MSY", "global_BH_MSY", "local_BH_MSY"); ignored for SPR-based methods. Default is all zeros (all fleets are landing fleets).

Value

A named list:

f_ref_pt: Numeric vector [n_regions]. Fishing mortality reference point by region. All regions share the same value for global methods; regions have independent values for local or independent methods.
b_ref_pt: Numeric array [n_pop, n_regions]. Equilibrium spawning biomass at the reference point by population and region (\(SBPR_F \times R_{eq}\) or \(SBPR_F \times \bar{R}\)).
virgin_b_ref_pt: Numeric array [n_pop, n_regions]. Virgin (unfished) spawning biomass by population and region (\(SBPR_0 \times R_0\) or \(SBPR_0 \times \bar{R}\)).
pop_b_ref_pt: Numeric array [n_pop, n_regions]. Population-specific effective spawning biomass at the reference point, evaluated at each population's natal region and incorporating stray contributions from other populations.
virgin_pop_b_ref_pt: Numeric array [n_pop, n_regions]. Population-specific effective virgin spawning biomass, evaluated at each population's natal region.

Compute fishing and biological reference points from an assessment or simulation

Usage

Arguments

Value

See also