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Setup tagging processes and parameters

Setup_Mod_Tagging.Rd

Setup tagging processes and parameters

Usage

Setup_Mod_Tagging(
  input_list,
  UseTagging = 0,
  tag_release_indicator = NULL,
  max_tag_liberty = 0,
  Tagged_Fish = NA,
  Obs_Tag_Recap = NA,
  Tag_LikeType = NA,
  mixing_period = 1,
  t_tagging = 0,
  tag_selex = NA,
  tag_natmort = NA,
  Use_TagRep_Prior = 0,
  TagRep_Prior = NULL,
  move_age_tag_pool = as.list(1:length(input_list$data$ages)),
  move_sex_tag_pool = as.list(1:input_list$data$n_sexes),
  Init_Tag_Mort_spec = NULL,
  Tag_Shed_spec = NULL,
  TagRep_spec = "fix",
  Tag_Reporting_blocks = NULL,
  ...
)

Arguments

input_list

List containing a data list, parameter list, and map list

UseTagging

Numeric (0 or 1) indicating whether to use tagging data (1) or not (0)

tag_release_indicator

Matrix [n_tag_cohorts x 2], where columns are release region and release year

max_tag_liberty

Maximum number of years to track a tagged cohort

Tagged_Fish

Array [n_tag_cohorts x n_ages x n_sexes] describing tagged fish releases

Obs_Tag_Recap

Array [max_tag_liberty x n_tag_cohorts x n_regions x n_ages x n_sexes] observed tag recaptures

Tag_LikeType

Character string specifying tag likelihood type. One of:

  • "Poisson"

  • "NegBin"

  • "Multinomial_Release"

  • "Multinomial_Recapture"

  • "Dirichlet-Multinomial_Release"

  • "Dirichlet-Multinomial_Recapture"

Example: Tag_LikeType = "NegBin"

mixing_period

Numeric indicating minimum years post-release to include in fitting

t_tagging

Fractional year when tagging occurs (e.g., 0.5 for mid-year)

tag_selex

Character string specifying tag recovery selectivity. One of:

  • "Uniform_DomFleet"

  • "SexAgg_DomFleet"

  • "SexSp_DomFleet"

  • "Uniform_AllFleet"

  • "SexAgg_AllFleet"

  • "SexSp_AllFleet"

Example: tag_selex = "SexSp_AllFleet"

tag_natmort

Character string specifying tag natural mortality parameterization. One of:

  • "AgeAgg_SexAgg"

  • "AgeSp_SexAgg"

  • "AgeAgg_SexSp"

  • "AgeSp_SexSp"

Example: tag_natmort = "AgeSp_SexSp"

Use_TagRep_Prior

Numeric (0 or 1) whether to use tag reporting rate prior

TagRep_Prior

Data frame containing prior specifications for tag reporting parameters. Must include columns: region (region index), block (time block index), mu (Numeric mean for tag reporting prior (normal space); NA if symmetric beta is used), sd (Numeric standard deviation for tag reporting prior (normal space)), and type (0 == symmetric beta, 1 == regular beta). Each row specifies a beta prior for one tag reporting parameter. Only parameters with rows in this data frame will have priors applied.

move_age_tag_pool

List or character specifying pooling of tagging data by age groups. Default does not pool ages. Examples:

  • list(1:5, 6:11, 12:20) pools these age groups together

  • "all" pools all ages together (internally converted to list(1:n_ages))

  • as.list(1:n_ages) fits each sex separately

move_sex_tag_pool

List or character specifying pooling of tagging data by sex groups. Default do not pool sexes. Examples:

  • list(1:2) pools sexes together

  • "all" pools all sexes together (internally converted to list(1:n_sexes))

  • list(1, 2) fits each sex separately

Init_Tag_Mort_spec

Character string "fix" or "est" specifying if initial tag mortality is fixed or estimated

Tag_Shed_spec

Character string "fix" or "est" specifying if chronic tag shedding is fixed or estimated

TagRep_spec

Character string specifying tag reporting rate estimation scheme:

  • "est_all" estimates rates for all blocks and regions independently

  • "est_shared_r" estimates rates shared across regions but varying by block

  • "fix" fixes all reporting rates (no estimation)

Tag_Reporting_blocks

Character vector specifying blocks of years and regions for tag reporting rates. Default is a single block for all regions. Format examples:

  • "Block_1_Year_1-15_Region_1"

  • "Block_2_Year_16-terminal_Region_2"

  • "none_Region_3" (means no block, constant for that region)

...

Additional starting values for tagging parameters such as ln_Init_Tag_Mort, ln_Tag_Shed, ln_tag_theta, Tag_Reporting_Pars

See also

Other Model Setup: Setup_Mod_Biologicals(), Setup_Mod_Catch_and_F(), Setup_Mod_Dim(), Setup_Mod_FishIdx_and_Comps(), Setup_Mod_Fishsel_and_Q(), Setup_Mod_Movement(), Setup_Mod_Rec(), Setup_Mod_SrvIdx_and_Comps(), Setup_Mod_Srvsel_and_Q(), Setup_Mod_Weighting()