Interface to Species Occurrence Data Sources
A programmatic interface to many species occurrence data sources,
including Global Biodiversity Information Facility ('GBIF'), 'USGSs'
Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist',
Berkeley 'Ecoinformatics' Engine, 'eBird', Integrated Digitized
'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information
System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes
functionality for retrieving species occurrence data, and combining
spocc (SPecies OCCurrence)
At rOpenSci, we have been writing R packages to interact with many sources of species occurrence data, including GBIF, Vertnet, BISON, iNaturalist, the Berkeley ecoengine, and eBird. Other databases are out there as well, which we can pull in.
spocc is an R package to query and collect species occurrence data from many sources. The goal is to to create a seamless search experience across data sources, as well as creating unified outputs across data sources.
spocc currently interfaces with nine major biodiversity repositories
Global Biodiversity Information Facility (GBIF) (via
rgbif) GBIF is a government funded open data repository with several partner organizations with the express goal of providing access to data on Earth's biodiversity. The data are made available by a network of member nodes, coordinating information from various participant organizations and government agencies.
Berkeley Ecoengine (via
ecoengine) The ecoengine is an open API built by the Berkeley Initiative for Global Change Biology. The repository provides access to over 3 million specimens from various Berkeley natural history museums. These data span more than a century and provide access to georeferenced specimens, species checklists, photographs, vegetation surveys and resurveys and a variety of measurements from environmental sensors located at reserves across University of California's natural reserve system.
iNaturalist iNaturalist provides access to crowd sourced citizen science data on species observations.
rvertnet) Similar to
rgbif, ecoengine, and
rbison(see below), VertNet provides access to more than 80 million vertebrate records spanning a large number of institutions and museums primarly covering four major disciplines (mammology, herpetology, ornithology, and icthyology).
Biodiversity Information Serving Our Nation (via
rbison) Built by the US Geological Survey's core science analytic team, BISON is a portal that provides access to species occurrence data from several participating institutions.
rebird) ebird is a database developed and maintained by the Cornell Lab of Ornithology and the National Audubon Society. It provides real-time access to checklist data, data on bird abundance and distribution, and communtiy reports from birders.
ridigbio) iDigBio facilitates the digitization of biological and paleobiological specimens and their associated data, and houses specimen data, as well as providing their specimen data via RESTful web services.
OBIS OBIS (Ocean Biogeographic Information System) allows users to search marine species datasets from all of the world's oceans.
Atlas of Living Australia ALA (Atlas of Living Australia) contains information on all the known species in Australia aggregated from a wide range of data providers: museums, herbaria, community groups, government departments, individuals and universities; it contains more than 50 million occurrence records.
The inspiration for this comes from users requesting a more seamless experience across data sources, and from our work on a similar package for taxonomy data (taxize).
BEWARE: In cases where you request data from multiple providers, especially when including GBIF, there could be duplicate records since many providers' data eventually ends up with GBIF. See
?spocc_duplicates, after installation, for more.
- spocc documentation: https://docs.ropensci.org/spocc/
- occurrence manual https://books.ropensci.org/occurrences/ a book in development on working with occurrence data in R
Stable version from CRAN
install.packages("spocc", dependencies = TRUE)
Or the development version from GitHub
- Please report any issues or bugs.
- License: MIT
- Get citation information for
spoccin R doing
citation(package = 'spocc')
- Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
- Sticker: Images come from Phylopic http://phylopic.org/
Functions in spocc
|as.obis||Coerce occurrence keys to obis id objects|
|as.gbif||Coerce occurrence keys to gbifkey/occkey objects|
|as.bison||Coerce occurrence keys to bisonkey/occkey objects|
|fixnames||Change names to be the same for each taxon.|
|as.vertnet||Coerce occurrence keys to vertnetkey/occkey objects|
|bbox2wkt||Convert a bounding box to a Well Known Text polygon, and a WKT to a bounding box|
|as.ecoengine||Coerce occurrence keys to ecoenginekey/occkey objects|
|as.ala||Coerce occurrence keys to ALA id objects|
|as.idigbio||Coerce occurrence keys to idigbio objects|
|as.inat||Coerce occurrence keys to iNaturalist id objects|
|inspect||Get more data on individual occurrences|
|occ_names||Search for species names across many data sources.|
|occ_coverage||Automatically generate coverages for a spocc search|
|spocc-package||Interface to many species occurrence data sources|
|spocc_duplicates||A note about duplicate occurrence records|
|spocc_objects||spocc objects and their print, plot, and summary methods|
|spocc_capwords||Capitalize the first letter of a character string.|
|occ_options||Look up options for parameters passed to each source|
|occ_names_options||Look up options for parameters passed to each source for occ_names function|
|wkt_vis||Visualize well-known text area's on a map.|
|occ||Search for species occurrence data across many data sources.|
|occ2df||Combine results from occ calls to a single data.frame|
Vignettes of spocc
Last month downloads
|License||MIT + file LICENSE|
|URL||https://github.com/ropensci/spocc (devel), https://docs.ropensci.org/spocc/ (user manual)|
|X-schema.org-keywords||specimens, API, web-services, occurrences, species, taxonomy, GBIF, INAT, BISON, Vertnet, eBird, Ecoengine, iDigBio, OBIS, ALA|
|Packaged||2020-07-31 18:57:29 UTC; sckott|
|Date/Publication||2020-07-31 19:20:03 UTC|
|imports||crul (>= 0.3.4) , data.table (>= 1.9.6) , jsonlite (>= 1.4) , lubridate (>= 1.5.0) , rbison (>= 0.6.0) , rebird (>= 1.0.0) , rgbif (>= 1.0.0) , ridigbio (>= 0.3.5) , rvertnet (>= 0.7.0) , tibble (>= 1.2) , utils , whisker (>= 0.3-2) , wicket (>= 0.4.0)|
|suggests||knitr , rmarkdown , taxize (>= 0.8.4) , testthat , vcr|
|Contributors||Karthik Ram, Ted Hart, rOpenSci|
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