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.

环境生物学家模拟生物体的生活地点，它们在空间中的分布（地理学）以及它们如何与当地环境相互作用，填充特定的生态位。 要进行这种建模，需要来自多个来源的数据和使用多个分析包：将这些数据整合到有用的工作流程中需要专业的技术能力。该提案将创建一个名为“Wallace”的软件应用程序，通过图形界面将数据和分析组件汇集在一起，使组件的选择更容易，保存工作流程，以便其他人可以对其进行修改，并为分析的最佳设置提供指导。它还将提供交互式地图、表格和图表，以探索结果。该应用程序被设计为易于扩展，该软件将通过Github作为开源，免费提供的资源进行管理。 在其他进步中，使用该软件的结果将导致更好地估计保护生物学，入侵物种和气候变化的影响。在环境生物学领域，具有和不具有强大编码技能的研究人员之间存在着巨大的差距：拟议的活动旨在缩小这一差距，使用创新的软件开发方法，可以改变这一领域。在初始阶段，该项目将发布软件应用程序“Wallace”，为新兴的利基/分布式建模领域提供最佳计算建模实践。该软件是一个模块化的Web应用程序（也可以在本地运行），通过图形用户界面（GUI）提供可定制的工作流程。它将使用最近开发的R包shiny构建，通过添加R包，它将允许轻松扩展到该领域目前正在生产的许多尖端方法。具体而言，华莱士将：1）利用来自在线数据库或用户输入的数据; 2）组装各种工具用于构建和评估模型; 3）为关键的概念和方法问题提供指导文本; 4）提供交互式地图，表格和图表，以查看和探索数据和模型预测; 5）在分析的每个阶段之后以多种形式提供结果供下载;以及6）提供用于在用户会话结束时重新运行整个分析的文档化的和可执行的代码。它的模块化性质将有助于其他研究人员在软件成熟时添加新的内容。

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.