Tag Recapture Likelihood — get_tag

Computes the negative log-likelihood for tag-recapture data using a seasonal, age-based model with beta-binomial distribution.

Usage

get_tag_like(
  tag_switch = 1,
  minK,
  n_K,
  n_T,
  n_I,
  n_J,
  first_yr,
  M_a,
  hrate_ysa,
  tag_release_cta,
  tag_recap_ctaa,
  minI,
  maxI,
  maxJ,
  shed1,
  shed2,
  tag_rep_rates_ya,
  tag_H_factor,
  tag_var_factor = 1.82
)

Arguments

tag_switch: Integer flag to turn the likelihood on (>0) or off (0).
minK: Integer starting cohort index.
n_K: Integer number of cohorts.
n_T: Integer number of tagging time periods.
n_I: Integer number of release ages.
n_J: Integer number of recapture ages.
first_yr: Integer first model year.
M_a: A vector of natural mortality rates indexed by age.
hrate_ysa: A 3D array of harvest rates with dimensions year by season by age.
tag_release_cta: A 3D array of tag release numbers with dimensions cohort by tagging period by release age.
tag_recap_ctaa: A 4D array of tag recapture numbers with dimensions cohort by tagging period by release age by recapture age.
minI: A vector of minimum release ages for each cohort.
maxI: A vector of maximum release ages for each cohort.
maxJ: A vector of maximum recapture ages for each cohort.
shed1: A vector of immediate tag shedding rates for each tagging period.
shed2: A vector of continuous tag shedding rates for each tagging period.
tag_rep_rates_ya: A matrix of tag reporting rates with dimensions year by age.
tag_H_factor: Numeric scaling factor for incomplete mixing in harvest rates (adjusts season 1 harvest).
tag_var_factor: Numeric overdispersion factor for beta-binomial distribution (default = 1.82).

Value

A list containing:

pred: 4D array of predicted tag recaptures.
resid: 4D array of standardized residuals.
lp: Vector of negative log-likelihood contributions for each independent likelihood component.