Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California, USA.
School of Mathematics and Statistics, University of Glasgow, Glasgow, UK.
Ecology. 2023 Jan;104(1):e3887. doi: 10.1002/ecy.3887. Epub 2022 Nov 30.
Spatial capture-recapture (SCR) is now routinely used for estimating abundance and density of wildlife populations. A standard SCR model includes sub-models for the distribution of individual activity centers (ACs) and for individual detections conditional on the locations of these ACs. Both sub-models can be expressed as point processes taking place in continuous space, but there is a lack of accessible and efficient tools to fit such models in a Bayesian paradigm. Here, we describe a set of custom functions and distributions to achieve this. Our work allows for more efficient model fitting with spatial covariates on population density, offers the option to fit SCR models using the semi-complete data likelihood (SCDL) approach instead of data augmentation, and better reflects the spatially continuous detection process in SCR studies that use area searches. In addition, the SCDL approach is more efficient than data augmentation for simple SCR models while losing its advantages for more complicated models that account for spatial variation in either population density or detection. We present the model formulation, test it with simulations, quantify computational efficiency gains, and conclude with a real-life example using non-invasive genetic sampling data for an elusive large carnivore, the wolverine (Gulo gulo) in Norway.
空间捕捉-再捕获 (SCR) 现在被常规用于估计野生动物种群的数量和密度。标准的 SCR 模型包括用于个体活动中心 (AC) 分布的子模型和用于在这些 AC 位置条件下个体检测的子模型。这两个子模型都可以表示为在连续空间中发生的点过程,但缺乏可访问和高效的工具来在贝叶斯范例中拟合此类模型。在这里,我们描述了一组自定义函数和分布来实现这一点。我们的工作允许在种群密度上对空间协变量进行更有效的模型拟合,提供了使用半完全数据似然 (SCDL) 方法而不是数据增强来拟合 SCR 模型的选项,并更好地反映了在使用区域搜索的 SCR 研究中,空间连续的检测过程。此外,SCDL 方法对于简单的 SCR 模型比数据增强更有效,而对于更复杂的模型,其在种群密度或检测的空间变化方面的优势则丧失。我们提出了模型公式,通过模拟进行了测试,量化了计算效率的提高,并以挪威一种难以捉摸的大型食肉动物——狼獾(Gulo gulo)的非侵入性遗传采样数据为例进行了总结。