1. Environmental DNA (eDNA) sampling is a promising tool for the detection of rare and cryptic taxa, such as aquatic pathogens, parasites and invasive species. Environmental DNA sampling workflows commonly rely on multi‐stage hierarchical sampling designs that induce complicated dependencies within the data. This complex dependence structure can be intuitively modelled with Bayesian multi‐scale occupancy models. However, current software for such models are computationally demanding, impeding their use.
2. We present an r package, msocc, that implements a data augmentation strategy to fit fully Bayesian, computationally efficient multi‐scale occupancy models. The msocc package allows users to fit multi‐scale occupancy models, to estimate and visualize posterior summaries of site, sample and replicate‐level occupancy, and to compare different models using Bayesian information criterion. Additionally, we provide a supplemental web application that allows users to investigate study design for multi‐scale occupancy models and acts as a graphical user interface to the msocc package.
3. The utility of the msocc package is illustrated on a published dataset and the functions in msocc are compared to the primary Bayesian toolkit for multi‐scale occupancy modelling, eDNAoccupancy, using various computational benchmarks. These benchmarks indicate that msocc is capable of fitting models 50 times faster than eDNAoccupancy.
4. We hope that access to software that efficiently fits, analyses and conducts study design investigations for multi‐scale occupancy models facilitates their implementation by the research and wildlife management communities.

中文翻译：

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msocc：在r中拟合和分析计算有效的多尺度占用模型

1. 环境DNA（eDNA）采样是检测稀有和隐性类群的有前途的工具，例如水生病原体，寄生虫和入侵物种。环境DNA采样工作流程通常依赖于多阶段的分层采样设计，这些设计会在数据中引起复杂的依赖性。可以使用贝叶斯多尺度占用模型直观地对这种复杂的依存关系模型进行建模。但是，当前用于此类模型的软件在计算上要求很高，从而阻碍了它们的使用。
2. 我们提出了一个r包msocc，该包实现了数据增强策略，以完全适合贝叶斯高效计算的多尺度占用模型。该msocc包允许用户以适应多尺度模型的占用，估计和可视化网站，样品和重复级占用后总结，并利用贝叶斯信息标准来比较不同的模型。此外，我们提供了一个补充性Web应用程序，使用户可以研究多尺度占用模型的研究设计，并充当msocc软件包的图形用户界面。
3. msocc软件包的实用性在已发布的数据集上进行了说明，并且使用各种计算基准，将msocc中的功能与主要的贝叶斯工具包进行了比较，以进行多尺度占用建模eDNAoccupancy。这些基准表明，msocc的模型拟合速度比eDNAoccupancy快50倍。
4. 我们希望能够访问能够有效拟合，分析和进行多尺度居住模型研究设计调查的软件，以促进研究和野生动植物管理社区的实施。