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.

文件LifeCycleModel.txt（MD5：245338d073342e885edb233f8fa7b050）说明

LifeCycleModel.txt是一段BUGS代码，用于估计完整生命周期模型的参数，该模型包含三部分内容：(i) 基于个体的仔鱼漂移与存活模型的输出结果——该模型可提供从产卵场到多个沿岸育苗场定居期间，鱼卵与仔鱼的扩散与死亡的年度估算值；(ii) 融合幼鱼拖网调查与地理信息系统（Geographic Information System）的栖息地适宜性模型，用于估算各育苗分区内的幼鱼密度与适宜幼鱼栖息地的表面积；(iii) 用于估算各龄组种群数量以及亚成体与成体捕捞死亡率的年龄结构统计捕捞模型。

本代码对应关联论文中测试的幼虫至幼鱼死亡过程的特定场景。该场景（R3）假定存在一个适用于所有育苗场的密度无关死亡参数（a_BH），以及各育苗场专属的密度依赖死亡参数（b_BH）。

代码中的注释行用于说明函数的输入与输出参数。该代码可通过OpenBUGS程序调用。