neotoma2: An R package to access data from the NeotomaPaleoecology Database
Socorro Dominguez Vidaña, Simon Goring
Abstract
The neotoma2 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 (Williams et al., 2018), containing nearly 9 million unique observations of paleoecological proxies with global coverage from 37 constituent databases.The package uses the Neotoma API v2.0 (Simon J. Goring, 2023) 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 get and set functions (e.g., get_sites(), set_sites()) respectively.This provides researchers with the opportunity to develop dynamic workflows that include data generated locally, and not yet submitted to the Neotoma database.The set functions are intended as a precursor to utilities to upload data directly to Neotoma, although this functionality is not yet available.The neotoma2 R package has been under dynamic development for over a year, but has been used for teaching and training (Simon J. Goring & Dominguez Vidaña, 2023).This release of the neotoma2 R package is a clean release of the package, with all of the core features provided and extensive test coverage implemented.