occcite

Querying database aggregators and citing primary sources of resulting occurrence records.

Science Score: 49.0%

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
Found 9 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
○
Committers with academic emails
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (18.8%) to scientific vocabulary

Keywords

biodiversity-data biodiversity-informatics biodiversity-standards citations museum-collection-specimens museum-collections museum-metadata

Last synced: 6 months ago · JSON representation

Repository

Querying database aggregators and citing primary sources of resulting occurrence records.

Basic Info

Host: GitHub
Owner: ropensci
License: gpl-3.0
Language: HTML
Default Branch: main
Homepage: https://docs.ropensci.org/occCite/
Size: 20.6 MB

Statistics

Stars: 23
Watchers: 4
Forks: 5
Open Issues: 9
Releases: 15

Topics

biodiversity-data biodiversity-informatics biodiversity-standards citations museum-collection-specimens museum-collections museum-metadata

Created over 7 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

occCite

Summary

The occCite workflow follows a three-step process. First, the user inputs one or more taxonomic names (or a phylogeny). occCite then rectifies these names by checking them against one or more taxonomic databases, which can be specified by the user (see the Global Names List). The results of the taxonomic rectification are then kept in an occCiteData object in local memory. Next, occCite takes the occCiteData object and user-defined search parameters to query BIEN (through rbien) and/or GBIF(through rGBIF) for records. The results are appended to the occCiteData object, along with metadata on the search. Finally, the user can pass the occCiteData object to occCitation, which compiles citations for the primary providers, database aggregators, and R packages used to build the dataset.

Please cite occCite. Run the following to get the appropriate citation for the version you’re using:

r citation(package = "occCite")

## 
## Owens H, Merow C, Maitner B, Kass J, Barve V, Guralnick R (2025).
## _occCite: Querying and Managing Large Biodiversity Occurrence
## Datasets_. doi: 10.5281/zenodo.4726676 (URL:
## https://doi.org/10.5281/zenodo.4726676), R package version 0.6.0,
## <URL: https://CRAN.R-project.org/package=occCite>.
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {occCite: Querying and Managing Large Biodiversity Occurrence Datasets},
##     author = {Hannah Owens and Cory Merow and Brian Maitner and Jamie Kass and Vijay Barve and Robert Guralnick},
##     year = {2025},
##     note = {R package version 0.6.0},
##     url = {https://CRAN.R-project.org/package=occCite},
##     doi = {10.5281/zenodo.4726676},
##   }

Installation:

r install.packages("occCite")

Or, install via r-universe

r install.packages("occCite", repos = "https://ropensci.r-universe.dev")

Or, install github development version:

r devtools::install_github("ropensci/occCite")

After using one of these options, you can load the package into your environment using:

r library("occCite")

Getting Started

occCite introduction vignette (https://ropensci.github.io/occCite/articles/a_Simple.html)
occCite advanced feature vignette (https://ropensci.github.io/occCite/articles/b_Advanced.html)
Function reference https://ropensci.github.io/occCite/reference/index.html
YouTube tutorial (https://www.youtube.com/watch?v=7qSCULN_VjY&t=17s)
Software note in Ecography (https://doi.org/10.1111/ecog.05618)

Meta

Please adhere to the ROpenSci code of conduct.
Please report any issues or bugs.
We encourage you to contribute to occCite! See the contributor guide for more information.
License: GPL-3
Get citation information for occCite in R using citation(package = 'occCite')

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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  "identifier": "occCite",
  "description": "Facilitates the gathering of biodiversity occurrence data from disparate sources. Metadata is managed throughout the process to facilitate reporting and enhanced ability to repeat analyses.",
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  "codeRepository": "https://github.com/ropensci/occCite",
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  "fileSize": "2590.942KB",
  "citation": [
    {
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      "datePublished": "2025",
      "author": [
        {
          "@type": "Person",
          "givenName": "Hannah",
          "familyName": "Owens"
        },
        {
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          "familyName": "Merow"
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  "keywords": [
    "biodiversity-informatics",
    "biodiversity-data",
    "biodiversity-standards",
    "citations",
    "museum-collections",
    "museum-metadata",
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  ]
}

GitHub Events

Total

Create event: 1
Issues event: 1
Release event: 1
Watch event: 3
Issue comment event: 2
Push event: 27
Fork event: 1

Last Year

Create event: 1
Issues event: 1
Release event: 1
Watch event: 3
Issue comment event: 2
Push event: 27
Fork event: 1

Committers

Last synced: about 2 years ago

All Time

Total Commits: 397
Total Committers: 7
Avg Commits per committer: 56.714
Development Distribution Score (DDS): 0.053

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
hannahlowens	h**s@g**m	376
Jamie Kass	j**s@g**m	7
Cory Merow	c**w@g**m	6
Vijay Barve	v**e@r**m	4
CORY MEROW	c**g@M**l	2
Maëlle Salmon	m**n@y**e	1
Gonzalo	g**b@g**m	1

Committer Domains (Top 20 + Academic)

rediffmail.com: 1

Issues and Pull Requests

Last synced: about 2 years ago

All Time

Total issues: 11
Total pull requests: 11
Average time to close issues: about 1 month
Average time to close pull requests: 15 days
Total issue authors: 3
Total pull request authors: 4
Average comments per issue: 0.18
Average comments per pull request: 0.27
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 0

Past Year

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

hannahlowens (10)
teunbrand (1)
gepinillab (1)
AMBarbosa (1)

Pull Request Authors

jamiemkass (5)
vijaybarve (3)
gepinillab (2)
maelle (1)

Top Labels

Issue Labels

Pull Request Labels

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
BIEN * imports
DBI * imports
RColorBrewer * imports
RPostgreSQL * imports
bib2df * imports
curl * imports
dplyr * imports
ggplot2 * imports
htmltools * imports
httr * imports
leaflet * imports
lubridate * imports
methods * imports
rgbif >= 3.1 imports
rlang * imports
stats * imports
stringr * imports
taxize * imports
tidyr * imports
viridis * imports
waffle * imports
RefManageR * suggests
ape * suggests
bit64 * suggests
covr * suggests
knitr * suggests
remotes * suggests
rmarkdown * suggests
testthat * suggests

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

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

.github/workflows/test-coverage.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v1 composite

.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