Set up the conventional tagging module for model fitting

Sets the release cohorts and recapture data, the tag likelihood, the mixing period, the release platform, which dims are attended and how they pool, and the reporting rate blocks, sharing and priors. Call after Setup_Mod_Dim.

Usage

Setup_Mod_Tagging(
  input_list,
  use_conv_fish_tagging = rep(0, input_list$data$n_fish_fleets),
  conv_tag_release_indicator = NULL,
  conv_tag_max_liberty = 0,
  conv_tagged_fish = NA,
  obs_conv_tag_fish_recap = NA,
  conv_fish_tag_like = NA,
  conv_tag_mixing_period = 1,
  conv_tag_t_tagging = 1,
  use_conv_tag_fishrep_prior = 0,
  conv_tag_fishrep_prior = NULL,
  conv_tag_pop_pool = as.list(1:input_list$data$n_pop),
  conv_tag_age_pool = as.list(seq_along(input_list$data$ages)),
  conv_tag_sex_pool = as.list(1:input_list$data$n_sexes),
  init_conv_tag_mort_spec = NULL,
  conv_tag_shed_spec = NULL,
  conv_tagrep_spec = "fix",
  conv_tag_fish_reporting_blocks = NULL,
  conv_fish_tag_attr = "p_a_s",
  conv_tag_release_platform = NULL,
  ...
)

Arguments

input_list: Named list with $data, $par, $map and $verbose.
use_conv_fish_tagging: Integer vector [n_fish_fleets] (0/1) of whether each fleet's tagging data enter the likelihood. Default 0.
conv_tag_release_indicator: Integer matrix [n_conv_tag_cohorts × 3] of the release region, year and season of each cohort. Required when any use_conv_fish_tagging = 1. Default NULL.
conv_tag_max_liberty: Integer maximum years at liberty in the likelihood; later recaptures are ignored. Must exceed 0 when tagging is active. Default 0.
conv_tagged_fish: Array [n_conv_tag_cohorts × n_pop × n_ages × n_sexes] of fish released per cohort. Dims not attended in conv_fish_tag_attr take all their fish in index 1 and zero elsewhere. Default NA.
obs_conv_tag_fish_recap: Observed recaptures [conv_tag_max_liberty × n_seas × n_conv_tag_cohorts × n_pop × n_regions × n_ages × n_sexes × n_fish_fleets]. Default NA.
conv_fish_tag_like: Tag recapture likelihood: "Poisson", "NegBin", "Multinomial_Release", "Multinomial_Recapture", "Dirichlet-Multinomial_Release" or "Dirichlet-Multinomial_Recapture", stored as 0-5. Default NA.
conv_tag_mixing_period: Integer years, or seasons in a seasonal model, after release before recaptures contribute to the likelihood, allowing the tags to mix before they inform movement. Default 1.
conv_tag_t_tagging: Numeric scalar or vector [n_conv_tag_cohorts] in $[0, 1]$, the fraction of the season remaining at release: 1 the start of the season, 0.5 mid-season, 0 the end. A scalar is recycled. Default 1.
use_conv_tag_fishrep_prior: Integer (0/1) for priors on the reporting rates. Default 0.
conv_tag_fishrep_prior: Data frame with columns region, block, fleet, mu, sd and type. Default NULL.
conv_tag_pop_pool, conv_tag_age_pool, conv_tag_sex_pool: Lists of integer vectors defining the population, age and sex pooling groups for the tagging likelihood. Use list(1:n) for a dim that is not attended; custom groupings such as list(1:5, 6:10) work for an attended one. A structure inconsistent with conv_fish_tag_attr warns and is overridden to a single group. Default one group per level.
init_conv_tag_mort_spec, conv_tag_shed_spec: "fix", "est_shared" or "est_all": whether the initial tag-induced mortality and the chronic shedding rate are held at their starting values, estimated as one value across release events, or estimated per event. See do_conv_init_tag_mort_mapping and do_conv_tag_shed_mapping. Default NULL.
conv_tagrep_spec: Sharing structure for conv_tag_fish_reporting_pars [n_regions × max_tagrep_blocks × n_fish_fleets]. Default "fix", which warns. See do_conv_tag_fish_reporting_pars_mapping.
conv_tag_fish_reporting_blocks: Character vector of time blocks for the fishery reporting rates, each "none_Region_r_Fleet_f" or "Block_b_Year_y1-y2_Region_r_Fleet_f" with "terminal" allowed as the end year. Parsed into an [n_regions × n_years × n_fish_fleets] array. NULL (default) gives one constant block per region and fleet.
conv_fish_tag_attr: Character scalar or vector [n_conv_tag_cohorts] naming which dims are resolved at release, built from "p" (population), "a" (age) and "s" (sex) joined by underscores: "p_a_s" (default), "a_s", "p_a", "p_s", "a", "s", "p" or "none". A scalar is recycled; a vector lets events resolve different dims. Region and fleet are always kept. An unattended dim takes all that event's fish in index 1 and is apportioned to full resolution by the release platform. A dim may only be split into several pooling groups if it is attended in every release event; otherwise its pooling argument is overridden to a single group with a warning.
conv_tag_release_platform: Character matrix [n_conv_tag_cohorts × 2] of the release platform and fleet index per cohort, in the format Setup_Sim_Tagging uses. Default NULL releases from the survey, fleet 1, which is read only when conv_fish_tag_attr leaves a dim of the released fish to be spread.
...: Optional starting values: ln_init_conv_tag_mort and ln_conv_tag_shed, each a scalar or a vector [n_conv_tag_cohorts] with a scalar recycled, default -1000; ln_conv_fish_tag_theta, default 0; and conv_tag_fish_reporting_pars [n_regions × max_tagrep_blocks × n_fish_fleets], default 0 on the logit scale, about a 0.5 reporting probability, with inactive fleet slots overwritten to -1000.

Value

input_list with the tagging configuration in $data, the starting values in $par for ln_init_conv_tag_mort and ln_conv_tag_shed (each of length n_conv_tag_cohorts, or 1 when tagging is inactive), ln_conv_fish_tag_theta and conv_tag_fish_reporting_pars, and the factor maps for all four in $map.

Set up the conventional tagging module for model fitting

Usage

Arguments

Value

See also