neotoma: A Programmatic Interface to the Neotoma Paleoecological Database
neotoma: A Programmatic Interface to the Neotoma Paleoecological Database
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DOI：
10.5334/oq.ab
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发表时间：
2015-01-01
期刊：
影响因子：
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通讯作者：
Williams, John W.
中科院分区：
文献类型：
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作者：
Goring, Simon;Dawson, Andria;Williams, John W.
古生态数据是生态和进化分析不可或缺的。首先，它们提供了一个机会，研究生态和进化的社区和非生物环境之间的相互作用跨越时间尺度。其次，它们使我们能够研究不经常发生的过程的长期结果，例如特大干旱，飓风和快速气候变化。第三，过去使我们能够在没有广泛人为影响的情况下研究生态过程。这里描述的R软件包（neotoma）从Neotoma古生态数据库（Neotoma数据库：http://www.neotomadb.org）获得并处理数据。Neotoma数据库是一个公共领域可搜索的存储库，用于存储过去500万年的多个古生态记录。Neotoma数据库提供了数据和网络基础设施，以研究从上新世到现在的物种和群落的时空动态;（neotoma）提供了一个用户界面，使这些研究成为可能。Neotoma使用可以包括位置、分类单元名称或数据集类型（例如，花粉，脊椎动物群，介形虫）使用数据库的应用程序接口（API）。该软件包返回一组与站点相关的嵌套元数据，包括完整的集合记录、用于重建年龄模型的地理年代学数据、数据集元数据（例如样本的年龄范围、进入Neotoma的日期、主要研究者）和站点元数据（例如位置、站点名称和描述）。（neotoma）还提供了工具，允许跨站点的分析，包括使用来自已发表的文献或用户提供的分类标准化的能力，分类（neotoma）包中的关键功能，可以使用，通过复制分析的例子，从已发表的文献，重点松迁移冰川消退和哺乳动物物种分布的变化在更新世。
Paleoecological data are integral to ecological and evolutionary analyses. First, they provide an opportunity to study ecological and evolutionary interactions between communities and abiotic environments across time scales. Second, they allow us to study the long-term outcomes of processes that occur infrequently, such as megadroughts, hurricanes, and rapid climate change. Third, the past allows us to study ecological processes in the absence of widespread anthropogenic influence.The R package (neotoma), described here, obtains and manipulates data from the NeotomaPaleoecological Database (Neotoma Database: http://www.neotomadb.org). The Neotoma Database is a public-domain searchable repository for multiproxypaleoecological records spanning the past 5 million years. The Neotoma Database provides the data and cyberinfrastructure to study spatiotemporal dynamics of species and communities from the Pliocene to the present; (neotoma) provides a user interface to enable these studies. neotoma searches the Neotoma Database using terms that can include location, taxon name, or dataset type (e.g., pollen, vertebrate fauna, ostracode) using the Database's Application Programming Interface (API). The package returns a set of nested metadata associated with the site, including the full assemblage record, geo-chronological data to enable the rebuilding of age models, dataset metadata (e.g. age range of samples, date of accession into Neotoma, principal investigator), and site metadata (e.g. location, site name and description). (neotoma) also provides tools to allow cross-site analysis, including the ability to standardize taxonomies using built-in taxonomies derived from the published literature or user-provided taxonomies.We show how key functions in the (neotoma) package can be used, by reproducing analytic examples from the published literature focusing on Pinus migration following deglaciation and shifts in mammal species distributions during the Pleistocene.