Supplement 1. Commented BUGS code that refers to scenario R3 with common αi’s and hierarchical βi’s.

File ListLifeCycleModel.txt (MD5: 245338d073342e885edb233f8fa7b050)Description LifeCycleModel.txt is a BUGS code to estimate parameters of a full life cycle model, including (i) outputs of an individual-based model for larval drift and survival that provided yearly estimates of the dispersion and mortality of eggs and larvae, from spawning grounds to settlement in several coastal nurseries; (ii) a habitat suitability model, based on juvenile trawl surveys coupled with a geographic information system, to estimate juvenile densities and surface areas of suitable juvenile habitat in each nursery sector; and (iii) a statistical catch-at-age model for the estimation of the numbers-at-age and the fishing mortality on subadults and adults. The present code refers to a specific scenario of the larvae to juvenile mortality process tested in the associated paper. This scenario (R3) assumes a density-independent mortality parameter common to all nurseries (a_BH) and a nursery-specific density-dependent mortality parameter (b_BH). Comment lines specify the inputs to the function and the outputs from the function. The code may be called from an OpenBUGS program.