wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions
wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions
复制标题
wallace 2：一款用于对物种生态位和分布进行建模的闪亮应用程序，经过重新设计以通过模块贡献促进扩展
DOI：
10.1111/ecog.06547
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发表时间：
2023
期刊：
影响因子：
5.9
通讯作者：
Cory M
中科院分区：
文献类型：
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作者：
Jamie M. Kass;Gonzalo E. Pinilla-Buitrago;Andrea Paz;Bethany A. Johnson;Valentina Grisales-Betancur;Sarah I. Meenan;Dean Attali;Olivier Broennimann;Peter J. Galante;Brian S. Maitner;Hannah L. Owens;Sara Varela;Matthew E. Aiello-Lammens;Cory M
4年前发布的Wallace Ecomodapp(R Packagewallace)提供了一个开放源码的交互平台，用于模拟物种利基和分布，作为可重复使用的工具箱和教育资源。Wallace利用文献中记录的R Package工具，并通过图形用户界面运行分析并返回代码以记录和复制它们。自发布以来，来自用户和合作伙伴的反馈帮助确定了需要改进的关键领域，从而导致了Wallace2的开发。根据通过社区扩展实现增长的愿景，核心开发团队与合作者进行了接触，并对应用程序进行了重大重组，以实现：简化添加自定义模块以扩展方法选择、在同一会议中对多个物种进行分析、改进元数据功能、新的数据库连接以及保存/加载会话。wallace2具有九个新模块和增加的功能，这些功能有助于从气候模拟、植物和古生物学数据库获取数据；定制数据输入；模型元数据跟踪；以及对R包的引用(以促进文件编制和向开发人员提供信用)。其中三个模块构成了环境空间分析的新组成部分(例如，生态位重叠)。在这一扩展的同时，还向生物地理学和生物多样性社区进行了外联，包括利用该软件的广泛指导文本进行国际介绍和讲习班。此外，这些改进还通过云计算实现扩展了可访问性，并包括一套全面的单元测试。Wallace2中的功能极大地改进了其可扩展性、分析广度和可重现性选项，包括使用新兴的元数据标准。新的体系结构通过展示直接的模块摄取和单元测试，为其他模块化软件提供了一个例子，特别是那些使用快速增长的R Packageshiny开发的软件。重要的是，wallace2为未来的扩张奠定了基础，包括那些能够进行生物多样性评估和保护威胁评估的扩张。
Released 4 years ago, theWallace EcoModapplication (R packagewallace) provided an open‐source and interactive platform for modeling species niches and distributions that served as a reproducible toolbox and educational resource.wallaceharnesses R package tools documented in the literature and makes them available via a graphical user interface that runs analyses and returns code to document and reproduce them. Since its release, feedback from users and partners helped identify key areas for advancement, leading to the development ofwallace2. Following the vision of growth by community expansion, the core development team engaged with collaborators and undertook a major restructuring of the application to enable: simplified addition of custom modules to expand methodological options, analyses for multiple species in the same session, improved metadata features, new database connections, and saving/loading sessions.wallace2 features nine new modules and added functionalities that facilitate data acquisition from climate‐simulation, botanical and paleontological databases; custom data inputs; model metadata tracking; and citations for R packages used (to promote documentation and give credit to developers). Three of these modules compose a new component for environmental space analyses (e.g., niche overlap). This expansion was paired with outreach to the biogeography and biodiversity communities, including international presentations and workshops that take advantage of the software's extensive guidance text. Additionally, the advances extend accessibility with a cloud‐computing implementation and include a suite of comprehensive unit tests. The features inwallace2 greatly improve its expandability, breadth of analyses, and reproducibility options, including the use of emerging metadata standards. The new architecture serves as an example for other modular software, especially those developed using the rapidly proliferating R packageshiny, by showcasing straightforward module ingestion and unit testing. Importantly,wallace2 sets the stage for future expansions, including those enabling biodiversity estimation and threat assessments for conservation.