Set up retained fishery selectivity

Sets the retention selectivity forms, time blocks, continuous time variation, process error, annual deviations and fixed or estimated parameters. Time variation through cont_tv_ret_sel and blocks through ret_sel_blocks are mutually exclusive within a fleet. Call 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,
  retsel_devs_shared_bins,
  ret_selex_type,
  use_fixed_ret_sel,
  ret_sel_input,
  ret_sel_bin_dev_bins = NULL,
  cont_tv_retsel_bin_devs = rep("none", input_list$data$n_fish_fleets),
  retsel_pe_wt = rep(1, input_list$data$n_fish_fleets),
  retsel_rw_init_sigma = rep(5, input_list$data$n_fish_fleets),
  retsel_dont_est_dev_first = rep(0, input_list$data$n_fish_fleets),
  ret_sel_nonpar_est_bins,
  ret_sel_sex_offset = rep("none", input_list$data$n_fish_fleets),
  ...
)

Arguments

input_list: Named list with $data, $par, $map and $verbose.
cont_tv_ret_sel: Character vector of continuous time variation per fleet, each "<type>_Fleet_<f>": "none", "iid", "rw", "3dmarg", "3dcond" or "2dar1". Stored as integer codes.
ret_sel_blocks: Character vector of discrete blocks, either "none_Fleet_<f>" or "Block_<b>_Year_<start>-<end>_Fleet_<f>" with "terminal" allowed as the end year. Expanded into an [n_regions × n_years × n_fish_fleets] array.
ret_sel_model: Character vector of the retention form per fleet, and optionally per block: "<type>_Fleet_<f>" or "<type>_Fleet_<f>_Block_<b>". The forms and their syntax are those of fish_sel_model in Setup_Mod_Fishsel_and_Q.
retsel_pe_pars_spec: Process error parameters for time-varying retention, one entry per fishery fleet.
ret_fixed_sel_pars_spec: Which fixed retention parameters are estimated.
ret_sel_devs_spec: Structure of the annual retention deviations per fleet.
ret_sel_corr_opt_semipar: Optional correlation structure for semi-parametric retention deviations, one entry per fishery fleet.
Use_ret_selex_prior: Integer flag (0/1) for retention selectivity priors.
ret_selex_prior: Data frame with columns region, fleet, block, sex, par, mu, sd and an optional type ("par" or "value"), as fish_selex_prior in Setup_Mod_Fishsel_and_Q.
retsel_devs_shared_bins: Bins sharing one retention deviation series.
ret_selex_type: Character scalar, "age" or "length".
use_fixed_ret_sel: Binary array [n_pop × n_regions × n_years × n_seas × n_fish_fleets], 1 to use ret_sel_input.
ret_sel_input: Fixed retention array [n_pop × n_regions × n_years × n_seas × n_bins × n_sexes × n_fish_fleets].
ret_sel_bin_dev_bins: List with one element per fleet naming the bins that fleet overrides, or NULL for none. An overridden bin takes a freely estimated annual value in place of what the functional form produced, applied after every other transformation including standardization. Default NULL.
cont_tv_retsel_bin_devs: Character vector [n_fish_fleets] of the process error on the bin-override deviations: "none" (default), "iid" or "rw".
retsel_pe_wt: Numeric vector [n_fish_fleets] multiplying the retention process error likelihood. Default 1. 0 skips that fleet's process error, so the deviations stay estimated but enter the objective only through the data and any smoothness or centering penalties. Values other than 0 or 1 make an estimated process error sigma reinterpretable. Applies to ln_retsel_devs only.
retsel_rw_init_sigma: Numeric vector [n_fish_fleets] giving the standard deviation of the first year of an "rw" deviation series. Default 5, which leaves that year effectively free. NA instead starts the walk at zero under the walk's own estimated sigma.
ret_sel_nonpar_est_bins: Estimated bins for non-parametric retention.
ret_sel_sex_offset: Character vector [n_fish_fleets] linking the sexes of a fleet's retention curve: "none" (default), "par", "scale" or "par_scale", as fish_sel_sex_offset in Setup_Mod_Fishsel_and_Q. Retention is a fraction, so a scale offset only makes sense where the scaled curve stays at or below one, and nothing enforces that.
...: Optional starting values for the selectivity parameters and deviations.

Value

input_list with the parsed retention structure arrays in $data, the starting values in $par and the factor maps in $map.

Usage

Arguments

Value

See also