TY - JOUR
T1 - Neotoma
T2 - A programmatic interface to the neotoma paleoecological database
AU - Goring, Simon
AU - Dawson, Andria
AU - Simpson, Gavin L.
AU - Ram, Karthik
AU - Graham, Russ W.
AU - Grimm, Eric C.
AU - Williams, John W.
N1 - Funding Information:
We would like to acknowledge the support of the rOpenSci project and the invaluable efforts made by data contributors across the globe who have provided the platform upon which Neotoma and the neotoma package are built. Brian Bills and Michael Anderson at Penn State University’s Center for Environmental Informatics of provided considerable support in helping us to understand and use the API. This paper is a product of the PalEON project (http://paleonproject.net), funded through the NSF-Macrosystems program grants #1065656, 1241868 and 1241874, and the Neotoma Paleoecology Database, funded by the NSF Geoinformatics program grants #0947459 and #0948652. GLS was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant Program (RGPIN 2014-04032). We would also like to thank Lee Hsiang Liow, Pasquale Raia and one anonymous reviewer for their helpful comments. The authors would also like to thank the staff at Ubiquity Press for their considerable efforts in working with the authors to provide a clean layout for the code presented in this paper.
Publisher Copyright:
© 2015 The Author(s).
PY - 2015
Y1 - 2015
N2 - 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 NeotomaPaleo-ecological 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.
AB - 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 NeotomaPaleo-ecological 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.
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U2 - 10.5334/oq.ab
DO - 10.5334/oq.ab
M3 - Article
AN - SCOPUS:84994532222
SN - 2055-298X
VL - 1
JO - Open Quaternary
JF - Open Quaternary
M1 - 2
ER -