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Resolve a modular selectivity penalty weight vector

resolve_sel_pen_wts.Rd

Converts a user-supplied selectivity penalty weight specification into the complete named weight vector consumed by Get_sel_PE_loglik and Get_Selex_Smoothness_Penalty. Preserves exact backward compatibility with the older single on/off cont_tv_*_sel_penalty flag (which only ever covered "yr_devs", "bin_curve", "yr_curve" – the process-error-deviation-based penalty terms used when a fleet has a continuous time-varying selectivity model active) when no explicit weights are supplied. Six additional "smooth_*" terms are included for Get_Selex_Smoothness_Penalty's modular terms, which operate directly on a fleet's realized selectivity surface and so apply to any selectivity functional form (not just the bicubic/cubic spline, Selex_Model == 8, that originally motivated them) – for example, a nonparametric (Selex_Model == 5) fleet with discrete time blocks (mirroring an ADMB assessment's "selectivity change years") can use these same terms to regularize curvature/stability across those blocks.

Usage

resolve_sel_pen_wts(pen_wts, penalty_flag)

Arguments

pen_wts

NULL, or a named numeric vector/list giving independent weights for any subset of "yr_devs", "bin_curve", "yr_curve", "smooth_bin_curve", "smooth_bin_diff", "smooth_yr_diff", "smooth_yr_curve", "smooth_dome", "smooth_mean_center". When supplied, any term not named is set to 0 (disabled) rather than falling back to penalty_flag – i.e. supplying pen_wts opts fully into the explicit, modular weight system rather than partially retaining the old implicit behavior.

penalty_flag

Logical. Used only when pen_wts is NULL: the legacy terms ("yr_devs", "bin_curve", "yr_curve") are set to 1 if TRUE, 0 if FALSE. The "smooth_*" terms are always 0 in this fallback, regardless of penalty_flag.

Value

Named numeric vector of length 9: c(yr_devs, bin_curve, yr_curve, smooth_bin_curve, smooth_bin_diff, smooth_yr_diff, smooth_yr_curve, smooth_dome, smooth_mean_center).