Calculate Tagging Likelihood (Version 1)

Usage

get_tag_like_v1(
  tag_switch,
  minK,
  n_K,
  n_T,
  n_I,
  n_J,
  first_yr,
  M_a,
  hrate_ysa,
  par_hstar_i,
  tag_release_cta,
  tag_recap_ctaa,
  minI,
  maxI,
  maxJ,
  shed1,
  shed2,
  tag_rep_rates_ya,
  tag_H_factor,
  tag_var_factor,
  tag_offset
)

Arguments

tag_switch: An integer scalar, switch to turn on (>0) or off (0) the tagging likelihood.
minK: An integer scalar, first tagged cohort index.
n_K: An integer scalar, number of tagged cohorts.
n_T: An integer scalar, number of tagger groups.
n_I: An integer scalar, number of release ages.
n_J: An integer scalar, number of recapture ages.
first_yr: An integer scalar, model start year.
M_a: A numeric vector of length n_age, natural mortality-at-age.
hrate_ysa: A numeric array of dimensions \[n_year + 1, n_season, n_age\], harvest rate.
par_hstar_i: A numeric vector, initial harvest rate parameters for tagged fish.
tag_release_cta: A numeric array of dimensions \[n_K, n_T, n_I\], tag releases by cohort, tagger, age.
tag_recap_ctaa: A numeric array of dimensions \[n_K, n_T, n_I, n_J\], tag recaptures.
minI: A numeric vector of length n_K, minimum release age by cohort.
maxI: A numeric vector of length n_K, maximum release age by cohort.
maxJ: A numeric vector of length n_K, maximum recapture age by cohort.
shed1: A numeric vector of length 6, immediate tag shedding rates by tagger.
shed2: A numeric vector of length 6, continuous tag shedding rates by tagger.
tag_rep_rates_ya: A numeric matrix, tag reporting rates by year and age.
tag_H_factor: A numeric scalar, harvest rate adjustment factor for tagged fish.
tag_var_factor: A numeric scalar, overdispersion factor for beta-binomial.
tag_offset: A numeric scalar, offset for likelihood calculation.

Value

A numeric scalar, total negative log-likelihood for tagging data.