CPUE index likelihood — get_cpue

Computes the likelihood for a standardized CPUE index using a log-linear model.

Usage

get_cpue_like(
  cpue_switch,
  cpue_a1 = 5,
  cpue_a2 = 17,
  cpue_years,
  cpue_obs,
  cpue_sd,
  cpue_sigma,
  cpue_omega,
  log_cpue_q,
  par_cpue_creep,
  number_ysa,
  sel_fya
)

Arguments

cpue_switch: Integer switch to activate the likelihood.
cpue_a1, cpue_a2: Minimum and maximum CPUE age indices.
cpue_years: a vector of year indices for CPUE observations.
cpue_obs: a vector of observed CPUE values.
cpue_sd: a vector of SDs associated with the observed CPUE values.
cpue_sigma: Process error standard deviation.
cpue_omega: Power parameter for scaling to total numbers.
log_cpue_q: Logarithm of catchability coefficient.
par_cpue_creep: Logarithm of catchability coefficient.
number_ysa: a 3D array year, season, age of numbers-at-age.
sel_fya: a 3D array of selectivity by fishery, year, and age.

Value

a list with predicted CPUE, residuals, and likelihood vector.