R Python, and Ruby clients for GBIF species occurrence data
Author and article information
Abstract
Background. The number of individuals of each species in a given location forms the basis for many sub-fields of ecology and evolution. Data on individuals, including which species, and where they're found can be used for a large number of research questions. Global Biodiversity Information Facility (hereafter, GBIF) is the largest of these. Programmatic clients for GBIF would make research dealing with GBIF data much easier and more reproducible.
Methods. We have developed clients to access GBIF data for each of the R, Python, and Ruby programming languages: rgbif, pygbif, gbifrb.
Results. For all clients we describe their design and utility, and demonstrate some use cases.
Discussion. Programmatic access to GBIF will facilitate more open and reproducible science - the three GBIF clients described herein are a significant contribution towards this goal.
Cite this as
2017. R Python, and Ruby clients for GBIF species occurrence data. PeerJ Preprints 5:e3304v1 https://doi.org/10.7287/peerj.preprints.3304v1Author comment
This is a preprint submission to PeerJ Preprints. We may submit to a journal for peer-review as well.
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Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Scott A Chamberlain conceived and designed the experiments, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Carl Boettiger conceived and designed the experiments, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
The source code for this paper is on GitHub at https://github.com/sckott/gbifms. The clients can be found at GitHub: R: https://github.com/ropensci/rgbif, Python: https://github.com/sckott/pygbif, Ruby: https://github.com/sckott/gbifrb
Funding
This project was supported in part by the Alfred P Sloan Foundation (Grant No. G-2014-13485), and in part by the Helmsley Foundation (Grant No. 2016PG-BRI004) The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
