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 or vector of length n_tag_rel_events (one value per row of conv_tag_release_indicator), each in $[0, 1]$. Fraction of the season remaining at the time of tag release for that release event. 1 = start of season; 0.5 = mid-season; 0 = end of season. A scalar is recycled to all release events. Default 1.

ln_init_conv_tag_mort

Log-scale initial tag-induced mortality applied at the moment of release. Numeric scalar or vector of length n_tag_rel_events, one value per release event. A scalar is recycled to all release events. Default -1000 (approximately zero mortality).

ln_conv_tag_shed

Log-scale annual chronic tag shedding rate. Numeric scalar or vector of length n_tag_rel_events, one value per release event. A scalar is recycled to all release events. Default -1000 (approximately no shedding).

conv_fish_tag_attr

Character scalar or character vector of length n_tag_rel_events specifying which biological dimensions are resolved at release (and hence retained at recapture) for each tag release event. A scalar is recycled to every event; a vector lets different events resolve different dimensions (e.g. event 1 known at "p_a_s", event 2 only at "p_a"). Each element is 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 (length n_tag_rel_events), $ln_init_conv_tag_mort (length n_tag_rel_events), $ln_conv_tag_shed (length n_tag_rel_events), $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