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<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.2 20190208//EN"
"JATS-publishing1.dtd">
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
<front>
<journal-meta>
<journal-id></journal-id>
<journal-title-group>
<journal-title>Journal of Open Source Software</journal-title>
<abbrev-journal-title>JOSS</abbrev-journal-title>
</journal-title-group>
<issn publication-format="electronic">2475-9066</issn>
<publisher>
<publisher-name>Open Journals</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">0</article-id>
<article-id pub-id-type="doi">N/A</article-id>
<title-group>
<article-title>neotoma2: An R package to access data from the Neotoma
Paleoecology Database</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-7926-4935</contrib-id>
<name>
<surname>Vidaña</surname>
<given-names>Socorro Dominguez</given-names>
</name>
<xref ref-type="aff" rid="aff-1"/>
</contrib>
<contrib contrib-type="author">
<contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-2700-4605</contrib-id>
<name>
<surname>Goring</surname>
<given-names>Simon J</given-names>
</name>
<xref ref-type="aff" rid="aff-2"/>
<xref ref-type="aff" rid="aff-3"/>
</contrib>
<aff id="aff-1">
<institution-wrap>
<institution>HT Data</institution>
</institution-wrap>
</aff>
<aff id="aff-2">
<institution-wrap>
<institution>Department of Geography, University of Wisconsin –
Madison</institution>
</institution-wrap>
</aff>
<aff id="aff-3">
<institution-wrap>
<institution>Center for Climatic Research, University of Wisconsin –
Madison</institution>
</institution-wrap>
</aff>
</contrib-group>
<pub-date date-type="pub" publication-format="electronic" iso-8601-date="2022-02-22">
<day>22</day>
<month>2</month>
<year>2022</year>
</pub-date>
<volume>¿VOL?</volume>
<issue>¿ISSUE?</issue>
<fpage>¿PAGE?</fpage>
<permissions>
<copyright-statement>Authors of papers retain copyright and release the
work under a Creative Commons Attribution 4.0 International License (CC
BY 4.0)</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>The article authors</copyright-holder>
<license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by/4.0/">
<license-p>Authors of papers retain copyright and release the work under
a Creative Commons Attribution 4.0 International License (CC BY
4.0)</license-p>
</license>
</permissions>
<kwd-group kwd-group-type="author">
<kwd>R</kwd>
<kwd>paleoecology</kwd>
<kwd>databases</kwd>
<kwd>paleoenvironment</kwd>
<kwd>Holocene</kwd>
<kwd>Pleistocene</kwd>
</kwd-group>
</article-meta>
</front>
<body>
<sec id="summary">
<title>Summary</title>
<p>The <monospace>neotoma2</monospace> R package is a tool to access
and manipulate data from the Neotoma Paleoecology Database
(https://www.neotomadb.org) within the R environment. Neotoma is a
community curated paleoecological data resource
(<xref alt="Williams et al., 2018" rid="ref-williams2018neotoma" ref-type="bibr">Williams
et al., 2018</xref>), containing nearly 9 million unique observations
of paleoecological proxies with global coverage from 37 constituent
databases. The package uses the Neotoma API v2.0
(<xref alt="Simon J. Goring, 2023" rid="ref-goring2023api" ref-type="bibr">Simon
J. Goring, 2023</xref>) as a tool to import records from the Neotoma
database, allowing researchers to examine taxonomic, spatial and
temporal patterns across space and time over the last 5.4 million
years. The R package allows researchers to download, and create new
records using <monospace>get_*()</monospace> (e.g.,
<monospace>get_sites()</monospace>) and <monospace>set_*()</monospace>
functions (e.g., <monospace>set_sites()</monospace>) respectively.
This provides researchers with the opportunity to develop dynamic
workflows that include data generated locally, and not yet submitted
to the Neotoma database.</p>
<p>The <monospace>neotoma2</monospace> R package has been under
dynamic development for over a year, but has been used for teaching
and training
(<xref alt="Simon J. Goring & Dominguez Vidaña, 2023" rid="ref-Goring2023APD" ref-type="bibr">Simon
J. Goring & Dominguez Vidaña, 2023</xref>). This release of the
<monospace>neotoma2</monospace> R package is a clean release of the
package, with all of the core features provided and extensive test
coverage implemented.</p>
</sec>
<sec id="statement-of-need">
<title>Statement of Need</title>
<p>The <monospace>neotoma</monospace> R package
(<xref alt="S. Goring et al., 2015" rid="ref-goring2015neotoma" ref-type="bibr">S.
Goring et al., 2015</xref>) leveraged the Neotoma Paleoeocology
Database v1.0 API and had been one of the primary tools for
researchers working with data from Neotoma
(<xref alt="Byun et al., 2021" rid="ref-byun2021extensive" ref-type="bibr">Byun
et al., 2021</xref>;
<xref alt="Kujawa et al., 2016" rid="ref-kujawa2016effects" ref-type="bibr">Kujawa
et al., 2016</xref>;
<xref alt="Wang et al., 2023" rid="ref-wang2023plants" ref-type="bibr">Wang
et al., 2023</xref>). Changes to the underlying database and a
rebuilding of the API required new data objects within the R package
to more closely align to the Neotoma data model
(<xref alt="Grimm, 2008" rid="ref-grimm2008neotoma" ref-type="bibr">Grimm,
2008</xref>). The broad user community for Neotoma
(<xref alt="Simon James Goring et al., 2018" rid="ref-goring2018nexus" ref-type="bibr">Simon
James Goring et al., 2018</xref>;
<xref alt="Williams et al., 2018" rid="ref-williams2018neotoma" ref-type="bibr">Williams
et al., 2018</xref>) requires a toolset that can access and manage
data for each of the more than 40 dataset types within Neotoma and so
extensive metadata must be accessed for each record. This package
conforms to a <monospace>tidyverse</monospace>
(<xref alt="Wickham et al., 2019" rid="ref-wickham2019tidyverse" ref-type="bibr">Wickham
et al., 2019</xref>) approach for data management, with data objects
that more closely resemble the underlying data model within Neotoma
(https://open.neotomadb.org/db_schema). Most importantly the
<monospace>neotoma2</monospace> package provides a toolset for
paleoecologists, ecologists, conservation ecologists, archaeologists,
and others, to access and examine the broad range of fossil data
contained within the Neotoma Paleoecology Database.</p>
</sec>
<sec id="acknowledgements">
<title>Acknowledgements</title>
<p>We acknowledge contributions from the Neotoma Paleoecology
Community, the participants of our workshops for the European Pollen
Database, American Quaternary Association and the International
Association of Limnologists/International Paleolimnology Association,
and members of the EarthCube community. This work was funded through a
grant to SJG from the National Science Foundation (NSF-1948926).</p>
</sec>
</body>
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