In chhetrid/rangemapR: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

Module: Query Database

BACKGROUND

Over the past two decades, the worldwide biodiversity informatics community has achieved remarkable progress, with many millions of species occurrence records now available online through various databases--including a substantial subset of records with assigned georeferences (e.g., latitude/longitude coordinates; Gaiji et al. 2013; Peterson et al. 2015; Walters and Scholes 2017). These data document the presence of a species at particular points in space and time, along with other useful metadata fields when available (e.g., institution, specimen/observation number, elevation, etc.). The origin of much of this information is specimens in research collections at natural history museums and herbaria, although newer data sources such as citizen-science initiatives are growing contributors as well (Sullivan et al. 2009).

IMPLEMENTATION

This module relies on the R package spocc, which provides streamlined access to many species occurrence databases, some of which aggregate data from myriad providers. Users can choose between three of the largest databases: GBIF, VertNet, and BISON. Note that currently users must choose only one of these databases, and any later download overwrites previous ones.

Records used in downstream analyses in Wallace are filtered to remove those without georeferences (latitude/longitude coordinates) and those that have exact duplicate coordinates of other records (including number of decimal places). The "Occs Tbl" tab displays all the filtered records with several key fields: name, longitude, latitude, year, institutionCode, country, stateProvince, locality, elevation, and basisOfRecord (standard field names from GBIF). The records available for download as a .csv file have all original fields and include records without georeferences.

REFERENCES

Gaiji, S., Chavan, V., Ariño, A. H., Otegui, J., Hobern, D., Sood, R., & Robles, E. (2013). Content assessment of the primary biodiversity data published through GBIF network: status, challenges and potentials. Biodiversity Informatics. 8: 94-172.

Peterson, A. T., Soberón, J., & Krishtalka, L. (2015). A global perspective on decadal challenges and priorities in biodiversity informatics. BMC Ecology. 15: 15.

Sullivan, B. L., Wood, C. L., Iliff, M. J., Bonney, R. E., Fink, D., & Kelling, S. (2009). eBird: A citizen-based bird observation network in the biological sciences. Biological Conservation. 142: 2282-2292.

Walters, M., and Scholes, R. J., (Eds.). (2017). The GEO Handbook on Biodiversity Observation Networks. Springer International Publishing. Link: http://link.springer.com/book/10.1007/978-3-319-27288-7

chhetrid/rangemapR documentation built on May 13, 2019, 11:09 a.m.