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https://github.com/ropensci/spocc
Species occurrence data toolkit for R
https://github.com/ropensci/spocc
antweb api bison data ebird ecoengine gbif idigbio inaturalist obis occurrence r r-package rstats species species-occurrence spocc vertnet
Last synced: 8 days ago
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Species occurrence data toolkit for R
- Host: GitHub
- URL: https://github.com/ropensci/spocc
- Owner: ropensci
- License: other
- Created: 2013-09-05T16:46:13.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2024-03-06T15:12:46.000Z (8 months ago)
- Last Synced: 2024-05-08T04:07:03.548Z (6 months ago)
- Topics: antweb, api, bison, data, ebird, ecoengine, gbif, idigbio, inaturalist, obis, occurrence, r, r-package, rstats, species, species-occurrence, spocc, vertnet
- Language: R
- Homepage: https://docs.ropensci.org/spocc
- Size: 13.9 MB
- Stars: 115
- Watchers: 21
- Forks: 27
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
- open-sustainable-technology - spocc - An R package to query and collect species occurrence data from many sources. (Biosphere / Biodiversity Data Access and Management)
README
# spocc (SPecies OCCurrence) 
[](https://github.com/ropensci/spocc/actions/workflows/R-CMD-check.yaml)
[](http://github.com/ropensci/spocc/actions?query=workflow%3Atest-sp-sf)
[](http://codecov.io/github/ropensci/spocc?branch=master)
[](http://cran.r-project.org/web/checks/check_results_spocc.html)
[](https://github.com/r-hub/cranlogs.app)
[](http://cran.r-project.org/package=spocc)
Docs:
At rOpenSci, we have been writing R packages to interact with many sources of species occurrence data, including [GBIF][gbif], [Vertnet][vertnet], [iNaturalist][inat], and [eBird][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)][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][inat]
iNaturalist provides access to crowd sourced citizen science data on species observations.
3. [VertNet][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][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][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]
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]
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][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:
## Contributing
See [CONTRIBUTING.md](http://github.com/ropensci/spocc/blob/master/.github/CONTRIBUTING.md)
## Installation
Stable version from CRAN
```r
install.packages("spocc", dependencies = TRUE)
```
Or the development version from GitHub
```r
install.packages("remotes")
remotes::install_github("ropensci/spocc")
```
```r
library("spocc")
```
## Make maps
All mapping functionality is now in a separate package [mapr](http://github.com/ropensci/mapr) (formerly known as `spoccutils`), to make `spocc` easier to maintain. `mapr` [on CRAN](http://cran.r-project.org/package=mapr).
## Meta
* Please [report any issues or bugs](http://github.com/ropensci/spocc/issues).
* License: MIT
* Get citation information for `spocc` in R doing `citation(package = 'spocc')`
* Please note that this package is released with a [Contributor Code of Conduct](http://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
* Sticker: Images come from Phylopic
[gbif]: http://www.gbif.org/
[vertnet]: http://github.com/ropensci/rvertnet
[inat]: http://www.inaturalist.org/
[taxize]: http://github.com/ropensci/taxize
[idigbio]: http://www.idigbio.org/
[obis]: http://obis.org/
[ebird]: http://ebird.org/home
[ala]: http://www.ala.org.au/