'Opakapaka Stock Assessment Parameters

A list of parameter values for the opakapaka stock assessment model, extracted from a fitted Stock Synthesis 3 (SS3) model and converted to opal conventions. Contains growth parameters, recruitment deviations, selectivity curves, and other model parameters suitable as starting values for RTMB optimization.

Usage

opaka_parameters

Format

A list with 14 named elements containing parameters extracted from SS3 model optimization and converted to opal conventions.

Source

Extracted from Stock Synthesis 3 parameter file (ss.par) and control file (control.ss_new). Growth parameters converted from standard VB to Schnute parameterization with A1 = 1, A2 = n_age.

Details

Parameter structure (14 list elements)

Stock parameters:

log_B0: Log initial recruitment/biomass (SS3's LN(R0)): 5.656
log_h: Steepness parameter (log-scale): log(0.76) = -0.274
log_sigma_r: Recruitment standard deviation (log-scale): log(0.52) = -0.654

Observation model parameters:

log_cpue_q: CPUE catchability coefficients (log-scale). Vector of length 2: -3.773 (Comm fleet), -6.253 (ResFish survey).
cpue_creep: CPUE creep adjustment: 0
log_cpue_tau: CPUE observation error (log-scale): -Inf (disabled)
log_cpue_omega: CPUE process error (log-scale): 0

Recruitment deviations:

rdev_y: Recruitment deviations by year (75 elements, annual timesteps 1949-2023). Extracted from SS3 estimated main recruitment deviations.

Selectivity parameters:

par_sel

Selectivity parameters matrix (3 fisheries x 6 columns).

Fleet 1 (Comm): Logistic. Cols 1-2 = inflection (36.1 cm), 95\
Fleet 2 (Non_comm): Logistic (fixed). Cols 1-2 = inflection (40 cm), 95\
Fleet 3 (ResFish): Double-normal (SS3 pattern 24). Cols 1-6 = peak (20.5), top_logit (-1.06), ascend_se (-0.34), descend_se (4.11), start_logit (-999), end_logit (-1.40).

Growth parameters (Schnute parameterization, log-scale):

log_L1: Log of length at reference age A1 = 1 (opal internal), corresponding to SS3 age 0: log(6.0) = 1.792
log_L2: Log of length at reference age A2 = 44 (opal internal), corresponding to SS3 age 43: log(67.498) = 4.212
log_k: Log of von Bertalanffy growth coefficient: log(0.242) = -1.419
log_CV1: Log of CV at young ages: log(0.085) = -2.465
log_CV2: Log of CV at old ages: log(0.085) = -2.465. Equal to log_CV1, giving constant CV across all lengths.

Examples

if (FALSE) { # \dontrun{
  data(opaka_parameters)
  str(opaka_parameters)
  # Access growth parameters on real scale
  exp(opaka_parameters$log_L1)   # L1 = 6.0 cm
  exp(opaka_parameters$log_L2)   # L2 = 67.5 cm
  exp(opaka_parameters$log_k)    # k = 0.242
  # Steepness
  exp(opaka_parameters$log_h)    # h = 0.76
} # }