CPUE index likelihood — get_cpue

Computes the likelihood for a standardized CPUE index using a log-linear model with optional technological creep adjustment.

Usage

get_cpue_like(
  cpue_switch = 1L,
  cpue_years,
  cpue_obs,
  cpue_sd,
  cpue_a1,
  cpue_a2,
  par_log_cpue_q,
  par_log_cpue_sigma,
  par_log_cpue_omega,
  par_cpue_creep,
  creep_init = 1L,
  number_ysa,
  sel_fya,
  cpue_q_years = NULL,
  cpue_sel_fishery = 7L
)

Arguments

cpue_switch: Integer flag for activation (0=off, >0=on).
cpue_years: A vector of year indices for each CPUE observation.
cpue_obs: A vector of observed CPUE values.
cpue_sd: A vector of observation standard deviations for each observation.
cpue_a1: Integer minimum age index for CPUE calculation.
cpue_a2: Integer maximum age index for CPUE calculation.
par_log_cpue_q: Numeric log-scale catchability coefficient(s).
par_log_cpue_sigma: Numeric log-scale process error SD.
par_log_cpue_omega: Numeric log-scale power parameter for scaling.
par_cpue_creep: Numeric technological creep rate.
creep_init: Numeric initial value for the technological creep adjustment (default = 1).
number_ysa: A 3D array of numbers-at-age with dimensions year by season by age.
sel_fya: A 3D array of selectivity values with dimensions fishery by year by age.
cpue_q_years: Optional model-year indices where each CPUE catchability block begins. Must have the same length as par_log_cpue_q when more than one q is estimated.
cpue_sel_fishery: Integer selectivity row used for the CPUE abundance index. The default, 7, uses the dedicated CPUE selectivity. This does not change the selectivity used by CPUE length compositions.

Value

A list containing:

unscaled: Vector of unscaled log-predictions (required for simulation).
pred: Vector of predicted CPUE values.
lp: Vector of negative log-likelihood contributions for each observation.