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spocc (SPecies OCCurrence)

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

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

At rOpenSci, we have been writing R packages to interact with many sources of species occurrence data, including GBIF, Vertnet, iNaturalist, 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 seven 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. iNaturalist iNaturalist provides access to crowd sourced citizen science data on species observations.

  3. VertNet (via rvertnet) Similar to rgbif (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).

  4. 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.

  5. 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.

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

  7. 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

spocc documentation: <docs.ropensci.org/spocc/>

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")

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.

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