Set up simulated tagging dynamics

Usage

Setup_Sim_Tagging(
  n_tags = NULL,
  n_tags_rel_input = NULL,
  UseTagging = 0,
  max_liberty = sim_list$n_ages/2,
  tag_release_indicator = expand.grid(regions = 1:sim_list$n_regions, tag_years =
    1:sim_list$n_yrs),
  t_tagging = 0,
  ln_Init_Tag_Mort = log(1e-05),
  ln_Tag_Shed = log(1e-05),
  Tag_Reporting_input = array(0.5, dim = c(sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_sims)),
  tag_selex = 5,
  tag_natmort = 3,
  tag_like = 0,
  ln_tag_theta = log(1),
  sim_list
)

Arguments

n_tags

Number of tags to release in a given year (scalar, default = NULL)

n_tags_rel_input

Number of tag releases by tag cohort length (default = NULL)

UseTagging

Boolean to use tagging (default = 0):

0: Do not simulate tagging
1: Simulate tagging

max_liberty

Maximum liberty to track cohorts (default = sim_list$n_ages / 2)

tag_release_indicator

Tag release indicator [regions × tag_years] (default = all combinations of regions × years via `expand.grid`)

t_tagging

Time of tagging (e.g., start year == 0, mid year == 0.5; default = 0)

ln_Init_Tag_Mort

Log initial tag-induced mortality (default = log(1e-5))

ln_Tag_Shed

Log chronic tag shedding rate (default = log(1e-5))

Tag_Reporting_input

Tag reporting input [n_regions × n_yrs × n_sims] (default = 0.5)

tag_selex

Tag selectivity type (integer, default = 5):

0: Uniform_DomFleet
1: SexAgg_DomFleet
2: SexSp_DomFleet
3: Uniform_AllFleet
4: SexAgg_AllFleet
5: SexSp_AllFleet

tag_natmort

Tag natural mortality type (integer, default = 3):

0: AgeAgg_SexAgg
1: AgeSp_SexAgg
2: AgeAgg_SexSp
3: AgeSp_SexSp

tag_like

Tag likelihood type (integer, default = 0):

0: Poisson
1: NegBin
2: Multinomial_Release
3: Multinomial_Recapture
4: Dirichlet-Multinomial_Release
5: Dirichlet-Multinomial_Recapture

ln_tag_theta

Scalar in log space describing tag likelihood overdispersion (default = log(1))

sim_list

Simulation list (required)

Set up simulated tagging dynamics

Usage

Arguments

See also