Get default initial parameter values — get

Gets a list of default initial values for the stock assessment model. Initial values are hand-coded from recent fitted assessment runs where available. Selectivity starts use the legacy v1-derived selectivity surface, then overlay recent fitted starts by matching the current data dimensions.

Usage

get_parameters(data)

Arguments

data: A list containing the data inputs for the model, including fishery-specific information, selectivity change years, and time-series data.

Value

A named list of initial parameter values containing:

par_log_B0: Numeric. Log-scale unfished biomass.
par_log_psi: Numeric. Log-scale psi parameter.
par_log_m0, par_log_m4, par_log_m10, par_log_m30, par_mc: Numeric. Natural-mortality parameters selected by data$M_switch.
par_log_h: Numeric. Log-scale steepness parameter.
par_log_sigma_r: Numeric. Log-scale recruitment standard deviation.
par_log_cpue_q, par_cpue_creep: Numeric. CPUE catchability coefficient(s) and creep parameter.
par_log_cpue_sigma, par_log_cpue_omega: Numeric. Log-scale CPUE observation error parameters.
par_log_aerial_tau: Numeric. Log-scale additional aerial-survey standard deviation.
par_log_aerial_sel: Numeric vector (length 2). Log-scale aerial selectivity parameters.
par_log_troll_tau: Numeric. Log-scale additional troll-survey standard deviation.
par_log_gt_q, par_log_hsp_q: Numeric. Log-scale catchability for gene-tagging and half-sibling-pair data.
pop_od, hsp_od, gt_od: Numeric. Fixed beta-binomial concentration parameters for parent-offspring, half-sibling, and gene-tagging data.
par_log_tag_H_factor: Numeric. Log-scale tagging mortality factor.
par_log_af_alpha: Numeric vector (length 2). Log-scale age-frequency alpha parameters.
par_log_lf_alpha: Numeric vector (length 5). Log-scale length-frequency alpha parameters.
par_sel_rho_y, par_sel_rho_a: Numeric vectors (length 7). Logit-scale selectivity temporal and age correlation parameters.
par_log_sel_sigma: Numeric vector (length 7). Log-scale selectivity standard deviations.
par_log_sel_1 through par_log_sel_7: Arrays. Log-scale selectivity by year and age for each fishery.
par_rdev_y: Numeric vector. Annual recruitment deviations.

Details

Current-model defaults set the additional aerial-survey standard deviation to 0.59, copy the fixed LL3 selectivity hyperparameters to LL4, and set the length-mortality exponent to -1 when data$M_switch = 2. The corresponding fixed or estimated treatment is defined by get_map().