Set up retained fishery selectivity

Configures all aspects of retained fishery selectivity and catchability for the estimation model, including functional forms, time blocks, continuous time-varying selectivity, process error structure, annual deviations, and fixed or estimated selectivity parameters. Must be called after Setup_Mod_FishIdx_and_Comps.

Usage

Setup_Mod_Retsel(
  input_list,
  cont_tv_ret_sel,
  ret_sel_blocks,
  ret_sel_model,
  retsel_pe_pars_spec,
  ret_fixed_sel_pars_spec,
  ret_sel_devs_spec,
  ret_sel_corr_opt_semipar,
  Use_ret_selex_prior,
  ret_selex_prior,
  cont_tv_ret_sel_penalty,
  retsel_devs_shared_bins,
  ret_selex_type,
  use_fixed_ret_sel,
  ret_sel_input,
  ret_sel_nonpar_est_bins,
  ...
)

Arguments

input_list

Named list containing $data, $par, $map, and $verbose sublists as created by upstream setup functions.

cont_tv_ret_sel

Character vector defining continuous time-varying selectivity structure per fleet. Format: "<type>_Fleet_<f>" where type is one of:

"none"

No time variation

"iid"

Independent year effects

"rw"

Random walk process

"3dmarg"

3D marginal structure

"3dcond"

3D conditional structure

"2dar1"

2D AR1 structure

Output is mapped to integer codes internally.

ret_sel_blocks

Character vector defining discrete selectivity blocks. Format: "none_Fleet_<f>" or "Block_<b>_Year_<start>-<end>_Fleet_<f>" (or terminal year version). Values are expanded into a 3D array: [n_regions × n_years × n_fish_fleets].

ret_sel_model

Character vector defining selectivity functional forms. Format: "<type>_Fleet_<f>" or "<type>_Fleet_<f>_Block_<b>". Supported types:

"logist1"

Logistic with \(a_{50}\) and slope \(k\) (2 parameters).

"logist2"

Logistic with \(a_{50}\) and \(a_{95}\) (2 parameters).

"gamma"

Dome-shaped gamma with \(a_{max}\) and \(\delta\) (2 parameters).

"exponential"

Exponential with a single power parameter (1 parameter).

"dbnrml"

Double-normal with 6 parameters.

"nonpar"

Non-parametric selectivity defined over discrete age or length bins, where selectivity is estimated as independent parameters (or grouped bins if specified via nonparametric bin mapping). No fixed functional form is imposed.

"asymplogist1"

Logistic selectivity with \(a_{50}\) and slope \(k\) and asymptotic control (3 parameters).

"asymplogist2"

Logistic selectivity with with \(a_{50}\) and \(a_{95}\) and asymptotic control (3 parameters).

retsel_pe_pars_spec

Specification of process error parameters for time-varying selectivity. Length must equal n_fish_fleets.

ret_fixed_sel_pars_spec

Specification controlling which fixed selectivity parameters are estimated vs fixed.

ret_sel_devs_spec

Specification of annual selectivity deviations structure per fleet.

ret_sel_corr_opt_semipar

Optional correlation structure for semi-parametric selectivity deviations. Length must equal n_fish_fleets.

Use_ret_selex_prior

Integer flag (0/1) indicating whether selectivity priors are used.

ret_selex_prior

Data frame of priors for selectivity parameters. Must include columns: region, fleet, block, sex, par, mu, sd.

cont_tv_ret_sel_penalty

Penalty value applied to continuous time-varying selectivity deviations.

retsel_devs_shared_bins

Vector defining shared bins for selectivity deviation estimation (e.g., age or length grouping structure).

ret_selex_type

Character string indicating selectivity domain: "age" or "length".

use_fixed_ret_sel

Binary indicator array [n_pop × n_regions × n_years × n_seas × n_fish_fleets]. 1 = use fixed selectivity input; 0 = estimate.

ret_sel_input

Fixed selectivity input array: [n_pop × n_regions × n_years × n_seas × (ages or lengths) × n_sexes × n_fish_fleets].

ret_sel_nonpar_est_bins

Vector defining estimated bins for non-parametric selectivity.

...

Optional starting values for selectivity parameters and deviations.

Value

The updated input_list with:

• Parsed selectivity structure arrays in $data

• Starting parameter arrays in $par

• Factor mapping objects in $map

Details

Selectivity time-variation via cont_tv_ret_sel and blocked selectivity via ret_sel_blocks are mutually exclusive within a fleet. Specifying both for the same fleet will result in an error.

See also

Other Model Setup: Setup_Mod_Biologicals(), Setup_Mod_Catch_and_F(), Setup_Mod_Dim(), Setup_Mod_Discard_Comps(), Setup_Mod_FishIdx_and_Comps(), Setup_Mod_Fishsel_and_Q(), Setup_Mod_Movement(), Setup_Mod_Rec(), Setup_Mod_SrvIdx_and_Comps(), Setup_Mod_Srvsel_and_Q(), Setup_Mod_Tagging(), Setup_Mod_Weighting()