EAGER: Making code-based analyses widely accessible for modeling species niches and distributions

EAGER：使基于代码的分析能够广泛用于建模物种生态位和分布

• 批准号: 1650241
• 负责人: Robert Anderson
• 金额: $ 6.09万
• 依托单位: CUNY City College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-15 至 2018-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1650241&HistoricalAwards=false
• 关键词: EAGER; Making; code; based; analyses

Environmental biologists model both where organisms live, their distribution in space (biogeography) and how they interact with the local environment, filling a particular niche. To do this modeling requires data from a number of sources and the use of multiple analytical packages: putting these together in useful workflows requires specialized technical abilities. This proposal will create a software application, called 'Wallace', that brings together the data and analytical components through a graphical interface to make selection of components easier, saves the workflow so others can rerun it, and provides guidance for the best settings for the analyses. It will also provide interactive maps, tables and graphs to explore the results. The application has been designed to be easily extended, and the software will be managed as an open-source, freely available resource through Github. Among other advances, results from using the software will lead to better estimates in conservation biology, invasive species, and the impact of climate change. A substantial divide exists in environmental biology between researchers with and without strong coding skills: the proposed activities aims to close that gap, using an innovative approach to software development that could transform the field. In the initial phase, The project will release the software application 'Wallace', to enable best computational modeling practices for the burgeoning field of niche/distributional modeling. This software is a modular web application (that also can be run locally) offering customizable workflows through a Graphical User Interface (GUI). It will be built using the recently developed R package shiny, which will allow easy extensibility to the many cutting-edge methods now being produced in the field, via the addition of R packages. Specifically, Wallace will: 1) harness data either from online databases or input by the user; 2) assemble a variety of tools for building and evaluating models; 3) give guidance text for critical conceptual and methodological issues; 4) feature interactive maps, tables, and graphs to view and explore data and model predictions; 5) offer results for download in multiple forms after each stage of the analysis; and 6) provide documented and executable code for rerunning the entire analysis at the end of a user session. Its modular nature will facilitate later addition of new elements by other researchers as the software matures.

环境生物学家在生物体居住的地方建模，它们在太空中的分布（生物地理学）以及它们如何与当地环境相互作用，并填充特定的利基市场。 要进行此模型，需要来自多个来源的数据和多个分析软件包的使用：将它们放在有用的工作流程中需要专门的技术能力。该建议将创建一个称为“华莱士”的软件应用程序，该应用程序通过图形接口将数据和分析组件汇总在一起，以使组件的选择更加容易，可以保存工作流程，以便其他人可以重新运行它，并为分​​析的最佳设置提供指导。它还将提供交互式图，表和图表来探索结果。该应用程序已设计为易于扩展，该软件将通过GitHub作为开源，可免费获得的资源管理。 除其他进步外，使用该软件的结果将导致更好地估计保护生物学，入侵物种以及气候变化的影响。具有和没有强大编码技巧的研究人员之间的环境生物学存在很大的鸿沟：拟议的活动旨在使用一种可以改变该领域的软件开发方法来缩小差距。在初始阶段，该项目将发布软件应用程序“ Wallace”，以启用最佳的计算建模实践，以促进利基/分销建模的新兴领域。该软件是一个模块化Web应用程序（也可以在本地运行），可通过图形用户界面（GUI）提供可自定义的工作流程。它将使用最近开发的R软件包Shiny构建，这将允许通过添加R软件包在现场生产的许多尖端方法易于扩展。具体来说，华莱士将：1）从在线数据库中利用数据或用户输入； 2）组装各种用于构建和评估模型的工具； 3）为关键的概念和方法论问题提供指导文本； 4）具有交互式图，表格和图形，以查看和探索数据和模型预测； 5）提供分析的每个阶段后以多种形式下载的结果； 6）提供记录的和可执行的代码，以在用户会话结束时重新分析整个分析。随着软件的成熟，它的模块化性质将有助于以后其他研究人员添加新元素。

项目成果

Opening the black box: an open-source release of Maxent

• DOI: 10.1111/ecog.03049
• 发表时间: 2017-07-01
• 期刊: ECOGRAPHY
• 影响因子: 5.9
• 作者: Phillips, Steven J.;Anderson, Robert P.;Blair, Mary E.
• 通讯作者: Blair, Mary E.