Stan code for a metapopulation model

The metapopulation model considers instream environmental conditions (i.e., for inferring habitat suitability) and landscape connectivity (i.e., via the river network and the terrestrial topography in terms of dispersal tendency among habitats in a long-term perspective), both of which can influence species occurrence at sampling sites (Chiu et al., 2020; DOI: 10.1016/j.scitotenv.2020.144045). Rather than actual measurements of species dispersal (e.g., by using drift and emergence trapping), spatial autocorrelation has been recognized as a robust component in the species distribution model and was adopted to model the dispersal tendency. Dispersal tendency is determined by spatial distance along inter-habitat pathway within the network. For determining the terrestrial connectivity, overland pathways across riverine habitats were created by least-cost path analysis.本集合种群模型（metapopulation model）考量了河流内生境环境条件（即用于推断生境适宜性）与景观连通性——后者从长期视角出发，依托河网与陆地地形表征生境间的扩散倾向——二者均可影响采样点位的物种出现情况（Chiu等，2020；DOI: 10.1016/j.scitotenv.2020.144045）。相较于采用漂流诱捕与羽化诱捕等手段开展的物种扩散实际观测，空间自相关（spatial autocorrelation）已被证实为物种分布模型中的稳健组成部分，因此被用于模拟扩散倾向。扩散倾向由网络内生境间通路的空间距离所决定。为确定陆地连通性，本研究通过最小成本路径分析（least-cost path analysis）构建了跨河流生境的陆地通路。