Collaborative Research: phyloregion, computational infrastructure for biogeographic regionalization and macroecology in the R computing environment

在共有生物区系的基础上进行地理比较，对于地理学研究和在地球气候迅速变暖的情况下管理生物多样性至关重要。然而，用于分析和处理大尺度物种地理数据的计算工具尚未完全开发。历史上，地理区域的分类是基于对区域生态、分类组成或植被特征的描述。最近的方法提供了更多的定量和客观的分类，但广泛概括了早期的努力，忽略了物种的共享系统发育关系所捕获的进化意义。由于地理学领域传统上是作为一门观察科学而不是实验科学发展起来的，因此将地理学的可复制分析工具开发成可复制的工作流程至关重要。为地理区划和宏观生态学而设计的R软件包RIGERATION可以克服这些计算挑战。它包含了地理区划，宏观生态学，保护和可视化的工具，并在各种学科，包括进化，微生物多样性，系统学，生态学，遗传学和许多其他潜在的应用。在该项目中，研究小组计划大幅提高生物区函数的计算效率，增加新功能，并创建一个用于生物地理学的用户指导软件开发模型。该项目将开发和实施生物区生物群落进化和生物地理学调查的新工具。建立了一种新的隶属度模型，该模型将采样单元表示为多个组中的部分隶属关系，以分析大型地理数据集。它将用新的工具来扩展生物地理学、宏观生态学和进化的可视化模式。Phyloregion将得到增强，可以在R和RevBayes（贝叶斯地理学的C++工具）之间传递对象，以便通过R进行地理可视化。最后，它将介绍新的保护工具，反映系统发育多样性的关键方面，包括丰富性，分歧和规律性。Phyloregion已经被广泛使用，并且是R中为megaphylogenies和macroecological数据集量身定制的少数地理资源之一。这项研究将创造新的，开源的，免费分发的软件工具，在地理学和超越变革的影响潜力。将利用讲习班和会议进行传播，并介绍中间R编码和地理工具的使用。研讨会将针对教师，博士后，特别是研究生和本科生的混合，他们将接受在研究中使用和应用RectorRegion的培训，并帮助开发自己的新颖的地理功能，以组装成R包。研究团队将与德克萨斯A M大学科珀斯克里斯蒂分校和东南大学现有的多样性项目合作，招募不同的本科生参与者，并为他们提供资源，以了解研究生院。该项目的所有产品将通过计算机代码、出版物、会议、讲习班和小册子免费和公开来源地传播。Phyloregion小插曲将被用来创建一个高年级的本科生和早期研究生课程。该赠款将支持一名博士后研究员和一名研究生和许多本科生的指导。将特别鼓励妇女和传统上代表性不足的群体申请博士后研究职位和讲习班。该地区项目可以在www.example.com上访问https://CRAN.R-project.org/package=phyloregionThis奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。

Establishing geographical comparisons based on shared biota is crucial to the study of biogeography and for managing biological diversity in the face of rapid warming of the Earth’s climate. However, the computational tools to analyze and manipulate the massive-scale species biogeography data has not been fully developed. Historically, classifications of biogeographic regions were based on descriptions of the ecology, taxonomic composition or vegetation features of regions. Recent approaches provided more quantitative, and objective classifications, but broadly recapitulated earlier efforts and overlooked the evolutionary implications captured by the shared phylogenetic relationships of species. Because the field of biogeography has traditionally developed as an observational science rather than an experimental one, developing replicable analytical tools for biogeography into reproducible workflows is critical. The R software package phyloregion – designed for biogeographic regionalization and macroecology – can overcome these computational challenges. It contains tools for biogeographical regionalization, macroecology, conservation, and visualization, and has potential application in various disciplines including evolution, microbial diversity, systematics, ecology, phylogenetics, and many others. In this project, the research team plans to substantially increase computational efficiency of functions in phyloregion, to add new functionality, and create a model for user-guided software development in biogeography.The project will develop and implement new tools in phyloregion for biome evolution and biogeographical investigations. Novel Grade of Membership model that represents sampling units as partial memberships in multiple groups will be established to analyze large biogeographic datasets. It will extend phyloregion with new tools to visualize patterns of biogeography, macroecology and evolution. Phyloregion will be enhanced to pass objects between R and RevBayes (a C++ tool for Bayesian phylogeography) for phylogeographic visualization through R. Finally, it will introduce new tools for conservation that reflect the key dimensions of phylogenetic diversity including richness, divergence and regularity. Phyloregion is already widely used and represents one of only a few biogeographical resources in R tailored for megaphylogenies and macroecological datasets. This research will create new, open-source, and freely distributed software tools with potential for transformative impact in biogeography and beyond. Workshops and conferences will be used for dissemination, and to provide introduction to intermediate R coding and implementation of biogeographical tools. Workshops will target a mix of faculty, postdocs, and especially graduate and undergraduate students, who will be trained on the use and application of phyloregion in their research, and to help develop their own novel biogeographic functions to assemble into an R package. The research team will work with existing diversity programs at Texas A&M University-Corpus Christi and Southeastern to recruit diverse undergraduate participants, and provide resources for them to learn about graduate school. All products from this project will be disseminated free and open-sourced through computer codes, publications, conferences, workshops and vignettes. Phyloregion vignettes will be used to create an upper-division course for undergraduate and early graduate students. The grant will support the mentoring of one postdoctoral researcher and a graduate student and many undergraduates. Women and traditionally underrepresented groups will be specifically encouraged to apply for the postdoctoral research position, as well as for the workshops. The phyloregion project can be accessed at https://CRAN.R-project.org/package=phyloregionThis award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.