TMB Directory Reference

Files
	bioenergetics.hpp
	ceattle.cpp
	The CEATTLE objective function: configuration, population dynamics, predation, likelihood and report.
	comp_osa.hpp
	One-step-ahead (OSA) residual helpers for composition data.
	comp_sim.hpp
	Random draws for composition-style observations, used by SIMULATE.
	diet_data.hpp
	growth.hpp
	helper_functions.hpp
	Small differentiable (AD-safe) utilities used across the CEATTLE template: numeric guards and transforms, the Dirichlet-multinomial density, and the separable year x age x cohort GMRF precision matrix (construct_Q).
	likelihood.hpp
	Likelihood math for section 13 of ceattle.cpp: the composition row density and linkage prior families that several terms share, and the composition plus-group fold.
	linkage.hpp
	predation.hpp
	recruitment.hpp
	selectivity.hpp
	spr.hpp
	Spawning biomass per recruit, for the Amendment-56 SPR proxies.