Compute fishing and biological reference points from an assessment or simulation

Builds the data list, calls the inner objective through RTMB, and returns the fishing and biological reference points a projection or control rule needs. Covers single-region and spatially explicit models, on SPR or Beverton-Holt MSY.

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,
  calc_rec_yrs = NULL,
  type,
  what,
  n_avg_yrs = 1,
  local_bh_msy_newton_steps = 6,
  is_discard_fleet = array(0, dim = data$n_fish_fleets)
)

Arguments

data

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

rep

SPoRC report object holding Fmort, fish_sel, natmort, Rec, SSB, h_trans, R0, rec_region_prop, rec_seas_prop, Movement and stray_rate.

SPR_x

Target spawning potential ratio, required under "SPR", "independent_SPR" and "global_SPR".

t_spawn

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

sex_ratio_f

Numeric array [n_pop, n_regions] of the female sex ratio at recruitment. Default 0.5.

calc_rec_st_yr

First model year in the mean historical recruitment the SPR biomass reference points are scaled by. The mean runs over calc_rec_st_yr:(n_years - rec_age). Default 1.

rec_age

Recruitment lag in years, the number of most recent years left out of that mean. Default 1.

calc_rec_yrs

Integer vector of model years (1 is the first model year) to average recruitment over instead, for a mean that runs to the terminal year or skips years. Overrides calc_rec_st_yr and rec_age when provided Default NULL.

type

Spatial structure. "single_region" has no movement and takes "SPR" or "MSY"; "multi_region" takes "independent_SPR", "independent_MSY", "global_SPR", "global_MSY" or "local_MSY".

what

Reference point method. "SPR" and "MSY" are the single-region \(F_{SPR_x}\) and Beverton-Holt \(F_{MSY}\). The "independent_" pair computes each region on its own without movement. "global_SPR" gives one shared \(F_{SPR_x}\) with movement, integrated across regions, and "global_MSY" the same for \(F_{MSY}\), single-population models only. "local_MSY" gives region-specific \(F_{MSY}\) values that jointly maximize total yield with movement, for single and multi-population models alike.

n_avg_yrs

Terminal years the demographic rates (selectivity, natural mortality, weight, maturity, movement) are averaged over first. Default 1.

local_bh_msy_newton_steps

Newton-Raphson iterations used to solve equilibrium recruitment by origin region under what = "local_MSY". Raise it if convergence is suspect. Default 6.

is_discard_fleet

Integer vector [n_fish_fleets], 1 for fleets whose catch is left out of landed yield while still contributing to \(Z\) and so to the population dynamics and spawning biomass. Read by the MSY methods only. Default all zeros.

Value

A named list holding f_ref_pt [n_regions], one value per region, shared across regions under the global methods; b_ref_pt [n_pop, n_regions], the equilibrium spawning biomass at the reference point (\(SBPR_F \times R_{eq}\) or \(SBPR_F \times \bar{R}\)); virgin_b_ref_pt, its unfished counterpart (\(SBPR_0 \times R_0\) or \(SBPR_0 \times \bar{R}\)); and pop_b_ref_pt and virgin_pop_b_ref_pt, the population-specific effective spawning biomass at each population's natal region, with the stray contributions from the other populations. mean_rec [n_pop, n_regions] is the mean recruitment over the averaged years, reported under every method although only the SPR methods scale by it.

See also

Other Reference Points and Projections: Do_Population_Projection(), Get_Reference_Point_Uncertainty(), get_key_quants()