spocc-package: Interface to many species occurrence data sources

Description Package API Currently supported species occurrence data sources Duplicates Clean data Make maps Author(s)


A programmatic interface to many species occurrence data sources, including GBIF, USGS's BISON, iNaturalist, Berkeley Ecoinformatics Engine, eBird, AntWeb, iDigBio, VertNet, OBIS, and ALA. Includes functionality for retrieving species occurrence data, and combining that data.

Package API

The main function to use is occ - a single interface to many species occurrence databases (see below for a list).

Other functions include:

  • occ2df - Combine results from occ into a data.frame

  • fixnames - Change names to be the same for each taxon

  • wkt_vis - Visualize WKT strings (used to define geometry based searches for some data sources) in an interactive map

Currently supported species occurrence data sources

Provider Web
GBIF http://www.gbif.org/
BISON https://bison.usgs.gov/
eBird http://ebird.org/content/ebird/
iNaturalist http://www.inaturalist.org/
Berkeley ecoengine https://ecoengine.berkeley.edu/
AntWeb http://www.antweb.org/
VertNet http://vertnet.org/
iDigBio https://www.idigbio.org/
OBIS http://www.iobis.org/
ALA http://www.ala.org.au/


See spocc_duplicates for more.

Clean data

All data cleaning functionality is in a new package: scrubr (https://github.com/ropensci/scrubr). On CRAN: https://cran.r-project.org/package=scrubr

Make maps

All mapping functionality is now in a separate package: mapr (https://github.com/ropensci/mapr) (formerly known as 'spoccutils'). On CRAN: https://cran.r-project.org/package=mapr


Scott Chamberlain myrmecocystus@gmail.com

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