ednaoccupancy: An r package for multiscale occupancy modelling of environmental DNA data
ednaoccupancy: An r package for multiscale occupancy modelling of environmental DNA data
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DOI：
10.1111/1755-0998.12735
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发表时间：
2018-03-01
影响因子：
7.7
通讯作者：
Erickson, Richard A.
中科院分区：
文献类型：
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作者：
Dorazio, Robert M.;Erickson, Richard A.
在这篇文章中，我们描述了ednaoccupancy，一个用于拟合贝叶斯多尺度占用模型的r包。这些模型适用于包括三个嵌套抽样水平的占用调查：研究区域内的主要样本单位，从每个主要单位收集的次要样本单位和每个次要样本单位的重复。这种设计通常用于环境DNA（eDNA）的占有调查。ednaoccupancy允许用户指定和拟合有或没有协变量的多尺度占用模型，估计发生和检测概率的后验总结，并使用贝叶斯模型选择标准比较不同的模型。我们通过分析两个已发表的数据集来说明这些功能：两栖动物真菌病原体的eDNA调查和濒危鱼类的eDNA调查。
In this article, we describe ednaoccupancy, an r package for fitting Bayesian, multiscale occupancy models. These models are appropriate for occupancy surveys that include three nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). ednaoccupancy allows users to specify and fit multiscale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model-selection criteria. We illustrate these features by analysing two published data sets: eDNA surveys of a fungal pathogen of amphibians and eDNA surveys of an endangered fish species.