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

环境生物学家对生物体生活在哪里、它们在空间中的分布(生物地理学)以及它们如何与当地环境相互作用进行建模，填补了一个特定的生态位。要做到这一点，建模需要来自多个来源的数据和多个分析包的使用：将这些放到有用的工作流程中需要专门的技术能力。这项提议将创建一个名为‘Wallace’的软件应用程序，它通过图形界面将数据和分析组件结合在一起，使组件选择更容易，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。它还将提供交互式地图、表格和图表来探索结果。该应用程序的设计易于扩展，该软件将通过Github作为开放源码的免费资源进行管理。在其他进展中，使用该软件的结果将导致对保护生物学、入侵物种和气候变化影响的更好估计。在环境生物学领域，拥有和没有强大编码技能的研究人员之间存在着巨大的分歧：拟议的活动旨在弥合这一差距，使用一种可能改变该领域的软件开发创新方法。在初始阶段，该项目将发布软件应用程序‘Wallace’，以支持利基/分布建模这一新兴领域的最佳计算建模实践。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目前在该领域生产的许多尖端方法。具体地说，华莱士将：1)利用来自在线数据库或用户输入的数据；2)汇编各种工具来构建和评估模型；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)在分析的每个阶段后以多种形式提供结果供下载；以及6)提供文档和可执行代码，用于在用户会话结束时重新运行整个分析。随着软件的成熟，它的模块化特性将有助于其他研究人员后来添加新的元素。

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.