A Bayesian nonparametric analysis of the 2003 outbreak of highly pathogenic avian influenza in the Netherlands
A Bayesian nonparametric analysis of the 2003 outbreak of highly pathogenic avian influenza in the Netherlands
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DOI：
10.1111/rssc.12515
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发表时间：
2021-08-10
影响因子：
1.6
通讯作者：
Hagenaars, Thomas J.
中科院分区：
文献类型：
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作者：
Seymour, Rowland G.;Kypraios, Theodore;Hagenaars, Thomas J.
农场的传染病对公共和动物健康都构成风险，因此了解它们如何在农场之间传播对于制定疾病控制策略以防止未来爆发至关重要。我们开发了新的贝叶斯非参数方法来拟合空间随机传播模型，其中任何两个农场之间的感染率是一个函数，取决于它们之间的距离，但没有假设一个指定的参数形式。在这种情况下进行非参数推断是具有挑战性的，因为观测数据的似然函数是难以处理的，因为基本的传输过程是不可观测的。我们采用一个完全贝叶斯的方法，通过分配一个转换高斯过程先验分布的感染率函数，然后开发一个有效的数据增强马尔可夫链蒙特卡罗算法进行贝叶斯推理。我们使用后验预测分布来模拟不同疾病控制方法的效果及其经济影响。我们分析了在荷兰的禽流感大爆发，并推断农场之间的感染率，以及未知的感染状况的农场被先发制人地扑杀。我们用我们的研究结果来分析环剔除策略，并得出结论，虽然有效，环剔除在高密度地区的影响有限。
Infectious diseases on farms pose both public and animal health risks, so understanding how they spread between farms is crucial for developing disease control strategies to prevent future outbreaks. We develop novel Bayesian nonparametric methodology to fit spatial stochastic transmission models in which the infection rate between any two farms is a function that depends on the distance between them, but without assuming a specified parametric form. Making nonparametric inference in this context is challenging since the likelihood function of the observed data is intractable because the underlying transmission process is unobserved. We adopt a fully Bayesian approach by assigning a transformed Gaussian process prior distribution to the infection rate function, and then develop an efficient data augmentation Markov Chain Monte Carlo algorithm to perform Bayesian inference. We use the posterior predictive distribution to simulate the effect of different disease control methods and their economic impact. We analyse a large outbreak of avian influenza in the Netherlands and infer the between-farm infection rate, as well as the unknown infection status of farms which were pre-emptively culled. We use our results to analyse ring-culling strategies, and conclude that although effective, ring-culling has limited impact in high-density areas.