neotoma: A Programmatic Interface to the Neotoma Paleoecological Database

Authors

  • Simon Goring University of Wisonsin-Madison
  • Andria Dawson University of California, Berkeley
  • Gavin L Simpson University of Regina
  • Karthik Ram University of California, Berkeley
  • Russ W Graham Pennsylvania State University
  • Eric C Grimm Illinois State Museum
  • John W Williams University of Wisconsin-Madison

DOI:

https://doi.org/10.5334/oq.ab

Keywords:

R software, neotoma, paleoecology, database, pollen, mammal

Abstract

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.

Author Biographies

Simon Goring, University of Wisonsin-Madison

Assistant Scientist

Department of Geography

University of Wisconsin-Madison

Andria Dawson, University of California, Berkeley

Department of Statistics
University of California, Berkeley
Berkeley, CA, USA

Gavin L Simpson, University of Regina

Institute of Environmental Change and Society, and Department of Biology,

University of Regina, Regina, SK, Canada

Karthik Ram, University of California, Berkeley

Berkeley Institute for Data Science

University of California, Berkeley

Berkeley, CA

Russ W Graham, Pennsylvania State University

Department of Geosciences

Pennsylvania State University

University Park, PA, USA

Eric C Grimm, Illinois State Museum

Research and Collections Center

Illinois State Museum

Springfield, IL, USA

John W Williams, University of Wisconsin-Madison

Department of Geography

Center for Climatic Research

University of Wisconsin-Madison

Madison, WI, USA

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Published

2015-03-09

Issue

Vol. 1 (2015)

Section

Methods

License

Copyright (c) 2015 The Author(s)

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