Data and code for 'Synergies between disease and urbanization drive the decline of threatened amphibian populations'

This archive provides all code and data necessary to reproduce the analyses in Heard et al. (submitted). 'Synergies between disease and urbanization drive the decline of threatened amphibian populations'. All code is in the form of R scripts, with scripts for the occupancy modelling itself, plus the fitting of the sub-models that contribute covariates to the occupancy model; namely, scripts for fitting the model of seasonal chytrid prevalence, site hydrology and dispersal probability between sites. An R script is also provided to complete the simulations to estimate equilibrium occupancy under the alternate scenarios considered in the paper. Model fitting relies on the MultiBUGS package, called from R. MultiBUGS is a parallel implementation of OpenBUGS (formerly WinBUGS) and allows for parallel computation of MCMC sampling. MultiBUGS can be found here: https://www.multibugs.org/本归档文件包含复现Heard等人（已投稿）论文《疾病与城市化的协同作用驱动受威胁两栖动物种群衰退》中所有分析所需的代码与数据。 所有代码均采用R脚本形式，包含占用模型（occupancy modelling）构建脚本，以及为占用模型提供协变量的子模型拟合脚本；具体涵盖季节性壶菌感染率拟合脚本、样地水文状况拟合脚本，以及样地间扩散概率拟合脚本。此外还提供了用于完成模拟的R脚本，以估算本文所探讨的各类替代情景下的平衡占用率。 模型拟合依赖于从R语言中调用的MultiBUGS软件包。MultiBUGS是OpenBUGS（前身为WinBUGS）的并行实现版本，支持马尔可夫链蒙特卡洛（Markov Chain Monte Carlo, MCMC）采样的并行计算。MultiBUGS的获取地址为：https://www.multibugs.org/