spocc v1.1.0

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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 those data.

Readme

spocc (SPecies OCCurrence)

R-check test-sp-sf codecov.io cran checks rstudio mirror downloads cran version

Docs: https://docs.ropensci.org/spocc/

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

  1. 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.

  2. 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.

  3. iNaturalist iNaturalist provides access to crowd sourced citizen science data on species observations.

  4. VertNet (via 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).

  5. 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.

  6. eBird (via 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.

  7. iDigBio (via 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.

  8. OBIS OBIS (Ocean Biogeographic Information System) allows users to search marine species datasets from all of the world's oceans.

  9. 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.

Learn more

Contributing

See CONTRIBUTING.md

Installation

Stable version from CRAN

install.packages("spocc", dependencies = TRUE)

Or the development version from GitHub

install.packages("remotes")
remotes::install_github("ropensci/spocc")
library("spocc")

Clean data

All data cleaning functionality is in a new package scrubr. scrubr on CRAN.

Make maps

All mapping functionality is now in a separate package mapr (formerly known as spoccutils), to make spocc easier to maintain. mapr on CRAN.

Meta

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Functions in spocc

Name Description
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
obis_search OBIS search
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Vignettes of spocc

Name
spocc.Rmd
spocc.Rmd.og
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Details

License MIT + file LICENSE
URL https://github.com/ropensci/spocc (devel), https://docs.ropensci.org/spocc/ (user manual)
BugReports https://github.com/ropensci/spocc/issues
LazyData true
VignetteBuilder knitr
Encoding UTF-8
Language en-US
RoxygenNote 7.1.1
X-schema.org-applicationCategory Biodiversity
X-schema.org-keywords specimens, API, web-services, occurrences, species, taxonomy, GBIF, INAT, BISON, Vertnet, eBird, Ecoengine, iDigBio, OBIS, ALA
X-schema.org-isPartOf https://ropensci.org
NeedsCompilation no
Packaged 2020-07-31 18:57:29 UTC; sckott
Repository CRAN
Date/Publication 2020-07-31 19:20:03 UTC

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