neotoma: A Programmatic Interface to the Neotoma Paleoecological Database

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, geochronological 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.

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