Here is a list of all files with brief descriptions:

[detail level 123]

src
TMB
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