r-rgbif

Interface to the Global Biodiversity Information Facility API

https://github.com/ropensci/rgbif

Science Score: 46.0%

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
Links to: zenodo.org
✓
Committers with academic emails
2 of 23 committers (8.7%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (15.6%) to scientific vocabulary

Keywords

api biodiversity data gbif lifewatch oscibio r r-package rstats species spocc

Keywords from Contributors

genome climate taxonomy taxize biology nomenclature darwincore mock http-mock noaa-data

Last synced: 6 months ago · JSON representation

Repository

Interface to the Global Biodiversity Information Facility API

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: master
Homepage: https://docs.ropensci.org/rgbif
Size: 154 MB

Statistics

Stars: 169
Watchers: 18
Forks: 51
Open Issues: 42
Releases: 53

Topics

api biodiversity data gbif lifewatch oscibio r r-package rstats species spocc

Created over 14 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Codemeta

rgbif

rgbif is an R package which gives you access to GBIF mediated data via its REST API.

GBIF (the Global Biodiversity Information Facility) is an international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.

Installation

r install.packages("rgbif") # CRAN version

r pak::pkg_install("ropensci/rgbif") # dev version

r install.packages("rgbif", repos="https://dev.ropensci.org") # dev version

Getting Started

There are several long-form articles that can help get you started:

Most GBIF users are interested in getting lat-lon occurrence records.

r occ_search(scientificName = "Pan troglodytes") occ_data(scientificName = "Pan troglodytes")

It is usually better to get occurrence records using a taxonKey. See the article Working With Taxonomic Names.

r taxonKey <- name_backbone("Pan troglodytes")$usageKey occ_search(taxonKey = taxonKey)

GBIF strongly recommends the use of occ_download() rather than occ_search() for serious research projects. See article Getting Occurrence Data From GBIF.

It is required to set up your GBIF credentials to make downloads from GBIF.

r occ_download(pred("taxonKey", 5219534)) # 5219534 is the taxonKey for Pan troglodytes

Citation

Under the terms of the GBIF data user agreement, users who download data agree to cite a DOI. Please see GBIF’s citation guidelines and Citing GBIF Mediated Data.

Please also cite rgbif by running citation(package = "rgbif").

Contributors

This list honors all contributors in alphabetical order. Code contributors are in bold.

adamdsmith - AgustinCamacho - AldoCompagnoni - AlexPeap - andzandz11 - AshleyWoods - AugustT - barthoekstra - benmarwick - cathynewman - cboettig - coyotree - damianooldoni - dandaman - djokester - dlebauer - dmcglinn - dmi3kno - dnoesgaard - DupontCai - ecology-data-science - EDiLD - elgabbas - emhart - fxi - ghost - gkburada - hadley - Huasheng12306 - ibartomeus - JanLauGe - jarioksa - jeroen - jhnwllr - jhpoelen - jivelasquezt - jkmccarthy - johnbaums - jtgiermakowski - jwhalennds - karthik - kgturner - Kim1801 - ljuliusson - ljvillanueva - luisDVA - martinpfannkuchen - MattBlissett - MattOates - maxhenschell - mdsumner - no-la-ngo - Octoberweather - omahs - Pakillo - peterdesmet - PhillRob - PietrH - poldham - qgroom - raymondben - rossmounce - sacrevert - sagitaninta - sckott - scottsfarley93 - simon-tarr - SriramRamesh - stevenpbachman - stevensotelo - stevenysw - TomaszSuchan - tphilippi - vandit15 - vervis - vijaybarve - willgearty - Xuletajr - yvanlebras - zixuan75

Meta

Please report any issues or bugs.
License: MIT
Get citation information for rgbif in R doing citation(package = 'rgbif')
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.

There are similar GBIF clients in other languages :

This package is part of spocc, along with several other packages, that provide access to occurrence records from multiple data sources.

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

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GitHub Events

Total

Create event: 13
Release event: 2
Issues event: 34
Watch event: 10
Delete event: 8
Issue comment event: 41
Push event: 55
Pull request review event: 14
Pull request review comment event: 28
Pull request event: 21
Fork event: 1

Last Year

Create event: 13
Release event: 2
Issues event: 34
Watch event: 10
Delete event: 8
Issue comment event: 41
Push event: 55
Pull request review event: 14
Pull request review comment event: 28
Pull request event: 21
Fork event: 1

Committers

Last synced: 7 months ago

All Time

Total Commits: 1,933
Total Committers: 23
Avg Commits per committer: 84.043
Development Distribution Score (DDS): 0.366

Past Year

Commits: 23
Committers: 5
Avg Commits per committer: 4.6
Development Distribution Score (DDS): 0.304

Top Committers

Name	Email	Commits
Scott Chamberlain	m**s@g**m	1,226
John Waller	f**2@k**k	234
John Waller	f**2@s**n	153
damianooldoni	d**i@i**e	138
John Waller	j**r@g**m	34
Laurens Geffert	l**t@g**m	32
Peter Desmet	p**k@g**m	30
VijayBarve	v**e@r**m	20
Karthik Ram	k**m@g**m	12
Matthew Blissett	m**t@b**k	12
Pieter Huybrechts	4****H	10
Jeroen Ooms	j**s@g**m	5
Daniel McGlinn	d**n@g**m	4
Dmytro Perepolkin	d**n@g**m	4
omahs	7****s	4
Sriram Ramesh	s**h@S**l	4
steven2249	s**w@b**u	3
Jari Oksanen	j**n@o**i	2
John	8****s	2
Ben Marwick	b**k@h**m	1
Maëlle Salmon	m**n@y**e	1
Michael Sumner	m**r@g**m	1
SriramRamesh	g**1@g**m	1

Committer Domains (Top 20 + Academic)

oulu.fi: 1 berkeley.edu: 1 blissett.me.uk: 1 rediffmail.com: 1 inbo.be: 1 science.domain: 1 ku.dk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 638
Total pull requests: 196
Average time to close issues: 2 months
Average time to close pull requests: 4 days
Total issue authors: 158
Total pull request authors: 21
Average comments per issue: 2.29
Average comments per pull request: 0.86
Merged pull requests: 174
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 36
Pull requests: 39
Average time to close issues: 22 days
Average time to close pull requests: 4 days
Issue authors: 15
Pull request authors: 2
Average comments per issue: 1.22
Average comments per pull request: 0.0
Merged pull requests: 30
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

sckott (287)
jhnwllr (118)
damianooldoni (18)
andzandz11 (8)
dnoesgaard (6)
peterdesmet (6)
veronicar239 (5)
dmcglinn (4)
AugustT (4)
Wolfudus (4)
maelle (4)
willgearty (4)
mikeroswell (3)
vijaybarve (3)
johnbaums (3)

Pull Request Authors

jhnwllr (144)
sckott (11)
damianooldoni (8)
peterdesmet (6)
stevenysw (4)
omahs (3)
johnbaums (3)
dmcglinn (2)
JanLauGe (2)
jarioksa (2)
PietrH (1)
jeroen (1)
zixuan75 (1)
luisDVA (1)
SriramRamesh (1)

Top Labels

Issue Labels

Bug (114) downloads (44) newapi (19) question (14) documentation (13) oldapi (11) idea (11) feature (9) maps-api (9) fromemail (8) queue (7) docs (6) noturgent (6) someday (4) windows (4) occ-issues (2) actions (1) duplicate (1) on-hold (1)

Pull Request Labels

maps-api (3) downloads (2) queue (2)

Packages

Total packages: 2
Total downloads: unknown

Total dependent packages: 2
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 73

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

Documentation: https://pkg.go.dev/github.com/ropensci/rgbif#section-documentation
License: other
Latest release: v3.8.3+incompatible
published 6 months ago

Versions: 55
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.5%

Average: 5.7%

Dependent repos count: 5.9%

Last synced: 6 months ago

conda-forge.org: r-rgbif

Homepage: https://github.com/ropensci/rgbif, https://ropensci.github.io/rgbif, https://ropensci.github.io/occurrence-manual
License: MIT
Latest release: 3.7.3
published over 3 years ago

Versions: 18
Dependent Packages: 2
Dependent Repositories: 1

Rankings

Dependent packages count: 19.6%

Dependent repos count: 24.1%

Average: 24.9%

Forks count: 25.4%

Stargazers count: 30.4%

Last synced: 6 months ago

Dependencies

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

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

.github/workflows/check-cron.yml actions

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

.github/workflows/revdep-check.yaml actions

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

DESCRIPTION cran

R6 * imports
conditionz * imports
crul >= 0.7.4 imports
data.table * imports
ggplot2 * imports
jsonlite >= 1.6 imports
lazyeval * imports
magrittr * imports
oai >= 0.2.2 imports
stats * imports
tibble * imports
whisker * imports
wk * imports
xml2 * imports
knitr * suggests
png * suggests
protolite >= 2.0 suggests
randgeo * suggests
raster * suggests
rmarkdown * suggests
sf * suggests
testthat * suggests
vcr >= 1.2.0 suggests

.github/workflows/rhub.yaml actions

r-hub/actions/checkout v1 composite
r-hub/actions/platform-info v1 composite
r-hub/actions/run-check v1 composite
r-hub/actions/setup v1 composite
r-hub/actions/setup-deps v1 composite
r-hub/actions/setup-r v1 composite