r-spocc

Species occurrence data toolkit for R

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
✓
Committers with academic emails
1 of 8 committers (12.5%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary

Keywords

antweb api bison data ebird ecoengine gbif idigbio inaturalist obis occurrence r r-package rstats species species-occurrence spocc vertnet

Keywords from Contributors

genome climate-data biomart database-retrieval ensembl-servers genome-annotation genome-retrieval meta-analysis metagenomics ncbi-genbank

Last synced: 4 months ago · JSON representation

Repository

Species occurrence data toolkit for R

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: master
Homepage: https://docs.ropensci.org/spocc
Size: 13.9 MB

Statistics

Stars: 121
Watchers: 20
Forks: 28
Open Issues: 18
Releases: 22

Topics

antweb api bison data ebird ecoengine gbif idigbio inaturalist obis occurrence r r-package rstats species species-occurrence spocc vertnet

Created over 12 years ago · Last pushed 11 months ago

Metadata Files

Readme Changelog Contributing License Codemeta

spocc (SPecies OCCurrence)

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

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

Learn more

spocc documentation:

Contributing

See 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 (formerly known as spoccutils), to make spocc easier to maintain. mapr on CRAN.

Meta

Please report any issues or bugs.
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. By contributing to this project, you agree to abide by its terms.
Sticker: Images come from Phylopic http://phylopic.org/

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

CodeMeta (codemeta.json)

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GitHub Events

Total

Issues event: 3
Watch event: 3

Last Year

Issues event: 3
Watch event: 3

Committers

Last synced: 5 months ago

All Time

Total Commits: 844
Total Committers: 8
Avg Commits per committer: 105.5
Development Distribution Score (DDS): 0.129

Past Year

Commits: 4
Committers: 2
Avg Commits per committer: 2.0
Development Distribution Score (DDS): 0.25

Top Committers

Name	Email	Commits
Scott Chamberlain	m**s@g**m	735
Karthik Ram	k**m@g**m	64
hannahlowens	h**s@g**m	23
Maëlle Salmon	m**n@y**e	12
Edmund Hart	e**t@g**m	5
Jeroen Ooms	j**s@g**m	2
David LeBauer	d**r@a**u	2
Stefan Widgren	s**n@g**m	1

Committer Domains (Top 20 + Academic)

arizona.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 243
Total pull requests: 23
Average time to close issues: 2 months
Average time to close pull requests: about 6 hours
Total issue authors: 42
Total pull request authors: 7
Average comments per issue: 2.49
Average comments per pull request: 0.83
Merged pull requests: 22
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 3
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

sckott (159)
emhart (13)
karthik (12)
maelle (10)
timcdlucas (4)
AMBarbosa (4)
jamiemkass (3)
Martin-Jung (2)
cboettig (2)
mgaynor1 (2)
remsamp (1)
Pakillo (1)
jenmark (1)
laeserman (1)
bw4sz (1)

Pull Request Authors

sckott (10)
karthik (4)
maelle (3)
hannahlowens (3)
stewid (1)
jessjaco (1)
dlebauer (1)

Top Labels

Issue Labels

bug (48) feature (15) question (11) maps (8) docs (7) datasource (7) idigbio (7) cleaning (5) metadata (2) dedup (2) tests (1)

Pull Request Labels

docs (1) feature (1)

Packages

Total packages: 2
Total downloads: unknown

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 31

proxy.golang.org: github.com/ropensci/spocc

Documentation: https://pkg.go.dev/github.com/ropensci/spocc#section-documentation
License: other
Latest release: v1.2.3
published almost 2 years ago

Versions: 26
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.5%

Average: 5.7%

Dependent repos count: 5.9%

Last synced: 4 months ago

conda-forge.org: r-spocc

Homepage: https://github.com/ropensci/spocc (devel), https://ropensci.github.io/spocc/ (user manual)
License: MIT
Latest release: 1.2.0
published almost 5 years ago

Versions: 5
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 24.1%

Dependent packages count: 29.0%

Average: 29.6%

Forks count: 32.3%

Stargazers count: 33.1%

Last synced: 4 months ago

Dependencies

DESCRIPTION cran

crul * imports
data.table * imports
jsonlite * imports
lubridate * imports
rbison * imports
rebird * imports
rgbif * imports
ridigbio * imports
rvertnet * imports
tibble * imports
utils * imports
wellknown * imports
whisker * imports
taxize * suggests
testthat * suggests
vcr * suggests

.github/workflows/test-sp-sf.yaml actions

actions/cache v1 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc master composite
r-lib/actions/setup-r master composite

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite