StoX: An open source software for marine survey analyses
StoX: An open source software for marine survey analyses
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DOI：
10.1111/2041-210x.13250
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发表时间：
2019-09-01
影响因子：
6.6
通讯作者：
Handegard, Nils Olav
中科院分区：
文献类型：
--
作者：
Johnsen, Espen;Totland, Atle;Handegard, Nils Olav
世界各地的科学家开展调查项目，以监测和表征丰度、种群结构、生物多样性和地理分布。为了评估海洋鱼类和浮游动物的状况，经常使用标准化的采样协议和分析技术每年重复进行种群调查，以建立可靠的种群状况。然而，尽管透明度和可重复性被认为是这一过程的重要原则，但通常很难获得元数据和数据处理步骤的全面文件。对于包含手动处理步骤的工作流来说，这尤其具有挑战性。StoX主要用于处理研究船的调查数据，我们还包括了几个标准的调查估计模型。该软件的开发是健壮和通用的，并针对开源社区，这样用户就可以轻松地构建自己的模型。StoX与R完全集成，以利用大量R包，并使任何StoX函数和种群估计模型能够使用R进行控制。对于研究船调查估计的免费软件有很大的需求，StoX在四大洲进行的调查中进行了测试，是许多重要鱼类种群调查的官方工具。StoX的基本工作流程和透明度原则，以及可定制的GUI，使StoX适用于任何地理编码的调查。StoX的未来版本将包括统计模型，以估计商业渔业的捕捞组成。在保护管理等领域，还需要记录估算方法，目前正在实施包括生物多样性指数在内的额外估算和分析模型。同时，我们设想与现有的国际和国家数据中心进行更紧密的web服务集成。
Scientists across the globe conduct survey programs to monitor and characterize abundance, population structure, biodiversity and geographical distributions. To assess the state of marine fish and zooplankton, population surveys are often repeated annually using standardized sampling protocols and analysis techniques to establish trustworthy stock status. However, although transparency and repeatability are recognised as important principles of this process, it is often difficult to obtain comprehensive documentation of metadata and data processing steps. This is particularly challenging for workflows that include manual processing steps. StoX was principally built to process research-vessel survey data, and we have included several standard survey estimation models. The software was developed to be robust and versatile and aimed at the open source community, such that users could easily build their own models. StoX is fully integrated with R to utilize the large number of R-packages and enable any StoX function and stock estimation model to be controlled using R. There has been a large need for a freely available software for research-vessel survey estimation, and StoX is tested in surveys carried out in four continents and is the official tool for many important fish stock surveys. The basic workflow and transparency principles of StoX, together with a customizable GUI, makes StoX applicable for any geographically coded surveys. Future versions of StoX will include statistical models to estimate the catch composition in commercial fisheries. In fields such as conservation management, there is also a need to document the estimation methods, and additional estimation and analyses models, including biodiversity indices are currently implemented. In parallel, we envision a closer web service integration with existing international and national data centres.