traits

R package for accessing species trait data from multiple databases

https://github.com/ropensci/traits

Science Score: 77.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: ncbi.nlm.nih.gov, zenodo.org
✓
Committers with academic emails
1 of 12 committers (8.3%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.4%) to scientific vocabulary

Keywords

api-client r r-package rstats species traits

Keywords from Contributors

genome biodiversity taxonomy meta-analysis biology mock geocode taxize noaa-data proteome

Last synced: 4 months ago · JSON representation ·

Repository

R package for accessing species trait data from multiple databases

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: master
Homepage:
Size: 4.47 MB

Statistics

Stars: 41
Watchers: 7
Forks: 13
Open Issues: 4
Releases: 8

Topics

api-client r r-package rstats species traits

Created over 11 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Contributing License Citation Codemeta

README.Rmd

---
title: "traits: Species Trait Data from Around the Web"
output: github_document
---

traits
=======

```{r echo=FALSE}
knitr::opts_chunk$set(
  comment = "#>",
  collapse = TRUE,
  warning = FALSE,
  message = FALSE
)
```


[![R-CMD-check](https://github.com/ropensci/traits/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/traits/actions/workflows/R-CMD-check.yaml)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/traits)](https://github.com/r-hub/cranlogs.app)
[![cran version](https://www.r-pkg.org/badges/version/traits)](https://CRAN.R-project.org/package=traits)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11224037.svg)](https://doi.org/10.5281/zenodo.11224037)

R client for various sources of species trait data.

Docs: https://docs.ropensci.org/traits/

What is a trait? A "trait" for the purposes of this package is broadly defined as an aspect of a species that can be described or measured, such as physical traits (size, length, height, color), behavioral traits (running speed, etc.), and even variables that make up the niche of the species (e.g., habitat).

Included in `traits` with the associated function prefix or function name:











  Souce
  Function prefix
  Link





  BETYdb
  betydb_
  https://www.betydb.org/


  NCBI
  ncbi_
  https://www.ncbi.nlm.nih.gov/


  Encylopedia of Life
  traitbank_
  





  Birdlife International
  birdlife_
  https://www.birdlife.org/


  LEDA Traitbase
  leda_
  


  Zanne et al. plant dataset
  tr_zanne
  


  Amniote life history dataset
  tr_ernest
  





Talk to us on the issues page (https://github.com/ropensci/traits/issues) if you know of a source of traits data with an API, and we'll see about including it.

## Installation

Stable R-Universe version

```{r eval=FALSE}
install.packages("traits", repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))
```

_Note: traits has been removed from CRAN pending https://github.com/ropensci/taxize/issues/938_

Or development version from GitHub

```{r eval=FALSE}
install.packages("traits", repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) 
remotes::install_github("ropensci/traits")
```

```{r}
library("traits")
library("dplyr")
```

## Contributors

* [Scott Chamberlain](https://github.com/sckott)
* [Zachary Foster](https://github.com/zachary-foster)
* [Ignasi Bartomeus](https://github.com/ibartomeus)
* [David LeBauer](https://github.com/dlebauer)
* [David Harris](https://github.com/davharris)
* [Chris Black](https://github.com/infotroph)
* [Rupert Collins](https://github.com/boopsboops)

## Meta

* Please [report any issues or bugs](https://github.com/ropensci/traits/issues).
* License: MIT
* Get citation information for `traits` in R doing `citation(package = 'traits')`
* Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.

[![ropensci_footer](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)

Souce	Function prefix	Link
BETYdb	`betydb_`	https://www.betydb.org/
NCBI	`ncbi_`	https://www.ncbi.nlm.nih.gov/
Encylopedia of Life	`traitbank_`
Birdlife International	`birdlife_`	https://www.birdlife.org/
LEDA Traitbase	`leda_`
Zanne et al. plant dataset	`tr_zanne`
Amniote life history dataset	`tr_ernest`

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

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "traits" in publications use:'
type: software
license: MIT
title: 'traits: Species Trait Data from Around the Web'
version: 0.5.2
abstract: Species trait data from many sources, including sequence data from 'NCBI'
  (<https://www.ncbi.nlm.nih.gov/>), plant traits from 'BETYdb', and data from 'EOL
  Traitbank' and 'Birdlife International'.
authors:
- family-names: LeBauer
  given-names: David
  email: dlebauer@gmail.com
  orcid: https://orcid.org/0000-0001-7228-053X
- family-names: Chamberlain
  given-names: Scott
  email: myrmecocystus@gmail.com
  orcid: https://orcid.org/0000-0003-1444-9135
- family-names: Foster
  given-names: Zachary
- family-names: Bartomeus
  given-names: Ignasi
- family-names: Black
  given-names: Chris
- family-names: Harris
  given-names: David
preferred-citation:
  type: manual
  title: 'traits: Species Trait Data from Around the Web'
  authors:
  - family-names: LeBauer
    given-names: David
    email: dlebauer@gmail.com
    orcid: https://orcid.org/0000-0001-7228-053X
  - family-names: Chamberlain
    given-names: Scott
    email: myrmecocystus@gmail.com
    orcid: https://orcid.org/0000-0003-1444-9135
  - family-names: Foster
    given-names: Zachary
  - family-names: Bartomeus
    given-names: Ignasi
  - family-names: Black
    given-names: Chris
  - family-names: Harris
    given-names: David
  year: '2025'
  notes: R package version 0.5.2, https://github.com/ropensci/traits, https://doi.org/10.5281/zenodo.11224037
  url: https://docs.ropensci.org/traits/
repository-code: https://github.com/ropensci/traits
url: https://docs.ropensci.org/traits/
date-released: '2025-04-10'
contact:
- family-names: LeBauer
  given-names: David
  email: dlebauer@gmail.com
  orcid: https://orcid.org/0000-0001-7228-053X
keywords:
- traits
- API
- web-services
- species
- taxonomy
- biodiversity
- ecology
- environmental-data
- species-traits
- api-client
- r
- r-package
- rstats

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GitHub Events

Total

Issues event: 7
Watch event: 1
Delete event: 3
Issue comment event: 3
Push event: 9
Pull request event: 5
Create event: 2

Last Year

Issues event: 7
Watch event: 1
Delete event: 3
Issue comment event: 3
Push event: 9
Pull request event: 5
Create event: 2

Committers

Last synced: 4 months ago

All Time

Total Commits: 341
Total Committers: 12
Avg Commits per committer: 28.417
Development Distribution Score (DDS): 0.343

Past Year

Commits: 9
Committers: 2
Avg Commits per committer: 4.5
Development Distribution Score (DDS): 0.222

Top Committers

Name	Email	Commits
Scott Chamberlain	m**s@g**m	224
David LeBauer	d**r@g**m	52
Chris Black	c**s@c**g	24
davharris	h**1@g**m	15
Nacho	n**o@a**r	12
rupert@sorubim	r**s@g**m	3
fosterz	z**9@g**m	3
Maëlle Salmon	m**n@y**e	2
Nick Heyek	n**k@p**m	2
github-actions[bot]	4****]	2
dschlaep	d**r@u**h	1
rOpenSci Bot	m**t@g**m	1

Committer Domains (Top 20 + Academic)

unibas.ch: 1 ckblack.org: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 89
Total pull requests: 27
Average time to close issues: over 1 year
Average time to close pull requests: about 1 month
Total issue authors: 23
Total pull request authors: 6
Average comments per issue: 2.82
Average comments per pull request: 2.26
Merged pull requests: 26
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 4
Average time to close issues: 4 months
Average time to close pull requests: about 14 hours
Issue authors: 2
Pull request authors: 1
Average comments per issue: 1.0
Average comments per pull request: 0.0
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

sckott (46)
dlebauer (9)
infotroph (6)
maelle (4)
mpnelsen (3)
zachary-foster (2)
ahhurlbert (2)
boopsboops (2)
mabarbour (1)
BenMerSci (1)
jeroen (1)
Rekyt (1)
rodrigo1406 (1)
kgturner (1)
serbinsh (1)

Pull Request Authors

dlebauer (20)
boopsboops (3)
zachary-foster (3)
infotroph (2)
ibartomeus (1)
dschlaep (1)

Top Labels

Issue Labels

datasource (15) bug (8) from-email (3) usecases (3) someday (2) question (1)

Pull Request Labels

Packages

Total packages: 3
Total downloads:
- cran 1,111 last-month
Total docker downloads: 172,057

Total dependent packages: 2
(may contain duplicates)
Total dependent repositories: 18
(may contain duplicates)
Total versions: 18
Total maintainers: 1

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

Documentation: https://pkg.go.dev/github.com/ropensci/traits#section-documentation
License: other
Latest release: v0.5.1
published over 3 years ago

Versions: 8
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

cran.r-project.org: traits

Species Trait Data from Around the Web

Homepage: https://docs.ropensci.org/traits/
Documentation: http://cran.r-project.org/web/packages/traits/traits.pdf
License: MIT + file LICENSE
Status: removed
Latest release: 0.5.1
published over 1 year ago

Versions: 8
Dependent Packages: 2
Dependent Repositories: 18
Downloads: 1,111 Last month
Docker Downloads: 172,057

Rankings

Docker downloads count: 0.0%

Forks count: 5.2%

Dependent repos count: 6.7%

Average: 7.6%

Stargazers count: 7.9%

Dependent packages count: 18.1%

Maintainers (1)

dlebauer@gmail.com

Last synced: 4 months ago

conda-forge.org: r-traits

Homepage: https://github.com/ropensci/traits
License: MIT
Latest release: 0.5.0
published over 5 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 38.2%

Average: 38.8%

Stargazers count: 39.3%

Last synced: 4 months ago

Dependencies

DESCRIPTION cran

R >= 2.10 depends
crul >= 0.6.0 imports
data.table >= 1.9.6 imports
hoardr * imports
httr >= 1.1.0 imports
jsonlite >= 0.9.19 imports
readr >= 1.1.1 imports
rvest imports
taxize >= 0.7.4 imports
tibble >= 1.3.4 imports
xml2 >= 0.1.2 imports
dplyr * suggests
knitr * suggests
plyr * suggests
rmarkdown * suggests
testthat * suggests

.github/workflows/update-citation-cff.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite