Set up conventional tagging dynamics for the operating model simulation

Populates sim_list with all conventional tagging inputs needed by the operating model: tag release cohort definitions, release platform, tagging timing, tag-induced mortality, chronic shedding, recapture likelihood settings, fishery reporting rates, and zero-filled containers for predicted and observed recaptures. Must be called after Setup_Sim_Dim.

Usage

Setup_Sim_Tagging(
  sim_list,
  n_tags = NULL,
  n_tags_rel_input = NULL,
  use_conv_fish_tagging = 0,
  conv_tag_max_liberty = sim_list$n_ages/2,
  conv_tag_release_indicator = expand.grid(regions = 1:sim_list$n_regions, tag_years =
    1:sim_list$n_yrs, tag_seas = 1:sim_list$n_seas),
  conv_tag_release_platform = matrix(c("survey", "1"), nrow =
    nrow(conv_tag_release_indicator), ncol = 2, byrow = TRUE, dimnames = list(NULL,
    c("platform", "fleet"))),
  conv_tag_t_tagging = 1,
  ln_init_conv_tag_mort = -1000,
  ln_conv_tag_shed = -1000,
  conv_fish_tag_attr = "p_a_s",
  conv_tag_fish_reporting_input = array(0.5, dim = c(sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_fish_fleets, sim_list$n_sims)),
  conv_fish_tag_like = 0,
  ln_conv_fish_tag_theta = log(1)
)

Arguments

sim_list

Simulation list returned by Setup_Sim_Dim.

n_tags

Numeric scalar. Constant number of tags released per release event. Cannot be specified simultaneously with n_tags_rel_input. Default NULL.

n_tags_rel_input

Array specifying cohort-specific tag release numbers (e.g., varying by length, age, or other structure). Overrides n_tags when supplied. Cannot be specified simultaneously with n_tags. Default NULL.

use_conv_fish_tagging

Integer (0/1). Whether conventional tag recaptures from fisheries are simulated. Default 0.

conv_tag_max_liberty

Integer. Maximum number of years-at-liberty tracked per tag cohort. Controls the size of recapture containers. Default: n_ages / 2.

conv_tag_release_indicator

Data frame defining tag release cohorts. Required columns: regions (release region), tag_years (release year), tag_seas (release season). Default: all combinations of regions, years, and seasons from sim_list.

conv_tag_release_platform

Character matrix [n_conv_tag_cohorts × 2] specifying the release platform and associated fleet index for each cohort. Rows must align with conv_tag_release_indicator. Column platform must be one of:

"population": Tags released directly into the population, independent of any fleet or survey sampling process. fleet column should be NA.
"fishery": Tags released through a fishery fleet. fleet column gives the fleet index.
"survey": Tags released through a survey fleet. fleet column gives the fleet index.

Default: "survey" platform with fleet 1 for every cohort.

conv_tag_t_tagging

Numeric scalar in $[0, 1]$. Fraction of the season remaining at the time of tag release. 1 = start of season; 0.5 = mid-season; 0 = end of season. Default 1.

ln_init_conv_tag_mort

Log-scale initial tag-induced mortality applied at the moment of release. Default -1000 (approximately zero mortality).

ln_conv_tag_shed

Log-scale annual chronic tag shedding rate. Default -1000 (approximately no shedding).

conv_fish_tag_attr

Character string specifying which biological dimensions are retained at recapture. Built from any combination of "p" (population), "a" (age), and "s" (sex), joined by underscores. Region and fleet are always retained. Valid values: "p_a_s", "a_s", "p_a", "p_s", "a", "s", "p", "none". Default "p_a_s".

conv_tag_fish_reporting_input

Fishery tag reporting rate array [n_regions × n_yrs × n_fish_fleets × n_sims]. Values represent the probability that a recaptured tag is reported and must be in $[0, 1]$. Default: 0.5 for all cells.

conv_fish_tag_like

Integer or character scalar specifying the tag recapture likelihood. Default 0 (Poisson). Options:

0/"Poisson": Poisson.
1/"NegBin": Negative binomial.
2/"Multinomial_Release": Multinomial conditioned on releases.
3/"Multinomial_Recapture": Multinomial conditioned on recaptures.
4/"Dirichlet-Multinomial_Release": Dirichlet-multinomial conditioned on releases.
5/"Dirichlet-Multinomial_Recapture": Dirichlet-multinomial conditioned on recaptures.

ln_conv_fish_tag_theta

Log-scale overdispersion parameter for negative-binomial (1) or Dirichlet-multinomial (4, 5) likelihoods. Ignored for Poisson and multinomial likelihoods. Default log(1).

Value

The input sim_list with tagging-related fields appended: $n_tags or $n_tags_rel_input (depending on which is provided), $conv_tag_max_liberty, $conv_tag_t_tagging, $ln_init_conv_tag_mort, $ln_conv_tag_shed, $conv_tag_release_indicator, $conv_tag_release_platform, $n_tag_rel_events, $use_conv_fish_tagging, $conv_fish_tag_like, $conv_fish_tag_attr, $ln_conv_fish_tag_theta, $conv_tag_fish_reporting, and zero-filled containers $conv_tagged_fish, $conv_tagged_fish_attr, $conv_tag_fish_avail, $obs_conv_tag_fish_recap, $pred_conv_tag_fish_recap.

Set up conventional tagging dynamics for the operating model simulation

Usage

Arguments

Value

See also