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Setup model objects for specifying recruitment module and associated processes

Setup_Mod_Rec.Rd

Setup model objects for specifying recruitment module and associated processes

Usage

Setup_Mod_Rec(
  input_list,
  rec_model,
  rec_dd = NULL,
  rec_lag = 1,
  Use_h_prior = 0,
  h_mu = NA,
  h_sd = NA,
  do_rec_bias_ramp = 0,
  bias_year = NA,
  max_bias_ramp_fct = 1,
  sigmaR_switch = 1,
  dont_est_recdev_last = 0,
  sexratio = 1,
  init_age_strc = 0,
  equil_init_age_strc = 1,
  init_F_prop = 0,
  sigmaR_spec = NULL,
  InitDevs_spec = NULL,
  RecDevs_spec = NULL,
  h_spec = NULL,
  t_spawn = 0,
  ...
)

Arguments

input_list

List containing data, parameters, and map lists used by the model.

rec_model

Character string specifying the recruitment model. Options are:

  • "mean_rec": Recruitment is a fixed mean value.

  • "bh_rec": Beverton-Holt recruitment with steepness parameter.

rec_dd

Character string specifying recruitment density dependence, options: "local", "global", or NULL.

rec_lag

Integer specifying the recruitment lag duration relative to spawning stock biomass (SSB).

Use_h_prior

Integer flag (0 or 1) indicating whether to apply a prior on steepness h.

h_mu

Numeric vector (length n_regions) specifying the mean steepness prior values if used.

h_sd

Numeric vector (length n_regions) specifying the standard deviation for steepness priors if used.

do_rec_bias_ramp

Integer flag (0 or 1) indicating whether to apply a recruitment bias correction ramp.

bias_year

Numeric vector of length 4 defining the recruitment bias ramp periods:

  • Element 1: End year of no bias correction period.

  • Element 2: End year of ascending bias ramp period.

  • Element 3: End year of full bias correction period.

  • Element 4: Start year of final no bias correction period.

For example, with 65 years total, c(21, 31, 60, 64) means:

  • Years 1–21: No bias correction.

  • Years 22–31: Ascending bias correction.

  • Years 32–60: Full bias correction.

  • Years 61–63: Descending bias ramp.

  • Years 64–65: No bias correction.

max_bias_ramp_fct

Numeric specifying the maximum bias correction to apply to the recruitment bias ramp (should be between 0 and 1)

sigmaR_switch

Integer year indicating when sigmaR switches from early to late values (0 disables switching).

dont_est_recdev_last

Integer specifying how many of the most recent recruitment deviations to not estimate. Default is 0.

sexratio

Numeric vector specifying recruitment sex ratio, dimensioned by number of sexes.

init_age_strc

Integer flag specifying initialization of initial age structure:

  • 0: Initialize by iteration.

  • 1: Initialize using a geometric series.

equil_init_age_strc

Integer flag specifying how initial age structure deviations should be initialized. Default is stochastic for all ages except the recruitment age and the plus group.

  • 0: Equilibrium initial age structure.

  • 1: Stochastic initial age structure for all ages, except for the plus group, which follows equilibrium calculations (geometric series)

  • 2: Stochastic initial age structure for all ages

init_F_prop

Numeric value specifying the initial fishing mortality proportion relative to mean fishing mortality for initializing age structure.

sigmaR_spec

Character string specifying estimation of recruitment variability (sigmaR):

  • NULL: Estimate separate sigmaR for early and late periods.

  • "est_shared": Estimate one sigmaR shared across periods.

  • "fix": Fix both sigmaR values.

  • "fix_early_est_late": Fix early sigmaR, estimate late sigmaR.

InitDevs_spec

Character string specifying estimation of initial age deviations:

  • NULL: Estimate deviations for all ages and regions.

  • "est_shared_r": Estimate deviations shared across regions.

  • "fix": Fix all deviations.

RecDevs_spec

Character string specifying recruitment deviation estimation:

  • NULL: Estimate deviations for all regions and years.

  • "est_shared_r": Estimate deviations shared across regions (global recruitment deviations).

  • "fix": Fix all recruitment deviations.

h_spec

Character string specifying steepness estimation:

  • NULL: Estimate steepness for all regions if rec_model == "bh_rec".

  • "est_shared_r": Estimate steepness shared across regions.

  • "fix": Fix steepness values.

If rec_model == "mean_rec", steepness is fixed.

t_spawn

Numeric fraction specifying spawning timing within the year.

...

Additional arguments specifying starting values for recruitment parameters such as ln_global_R0, Rec_prop, h, ln_InitDevs, ln_RecDevs, and ln_sigmaR.