r-taxize

A taxonomic toolbelt for R

https://github.com/ropensci/taxize

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
4 of 44 committers (9.1%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (14.6%) to scientific vocabulary

Keywords

api api-wrapper biodiversity biology darwincore data nomenclature r r-package rstats taxize taxonomy

Keywords from Contributors

genome ecology weather-data data-access sequence temperature carpentries tidyverse data-carpentry weather

Last synced: 4 months ago · JSON representation

Repository

A taxonomic toolbelt for R

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: master
Homepage: https://docs.ropensci.org/taxize
Size: 36.6 MB

Statistics

Stars: 286
Watchers: 32
Forks: 63
Open Issues: 53
Releases: 42

Topics

api api-wrapper biodiversity biology darwincore data nomenclature r r-package rstats taxize taxonomy

Created over 14 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog Contributing License Codemeta

README.Rmd

---
output: github_document
---

taxize
======

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

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![rworkflows](https://github.com/ropensci/taxize/workflows/rworkflows/badge.svg)](https://github.com/ropensci/taxize/actions/)
[![codecov](https://codecov.io/gh/ropensci/taxize/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/taxize)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/taxize)](https://github.com/r-hub/cranlogs.app)
[![cran version](https://www.r-pkg.org/badges/version/taxize)](https://cran.r-project.org/package=taxize)


`taxize` allows users to search over many taxonomic data sources for species names (scientific and common) and download up and downstream taxonomic hierarchical information - among other things.


Package documentation: https://docs.ropensci.org/taxize/


## Installation

### Stable version from CRAN

```{r eval=FALSE}
install.packages("taxize")
```

### Development version from GitHub

Windows users install Rtools first.

```{r eval=FALSE}
install.packages("remotes")
remotes::install_github("ropensci/taxize")
```

```{r}
library('taxize')
```

## Screencast



## Contributing

See our [CONTRIBUTING](https://github.com/ropensci/taxize/blob/master/.github/CONTRIBUTING.md) document.

## Contributors

Collected via GitHub Issues: honors all contributors in alphabetical order. Code contributors are in bold.

afkoeppel - ahhurlbert - albnd - Alectoria - andzandz11 - **anirvan** - antagomir - **arendsee** - ArielGreiner - arw36 - ashenkin - **ashiklom** - benjaminschwetz - **benmarwick** - bienflorencia - binkySallly - bomeara - BridgettCollis - bw4sz - **cboettig** - cdeterman - ChrKoenig - chuckrp - clarson2191 - claudenozeres - cmzambranat - cparsania - daattali - DanielGMead - DarrenObbard - davharris - davidvilanova - diogoprov - **dlebauer** - dlenz1 - dougwyu - dschlaep - **EDiLD** - edwbaker - emhart - eregenyi - fdschneider - fgabriel1891 - fischhoff - **fmichonneau** - **fozy81** - **gedankenstuecke** - gimoya - git-og - glaroc - **gpli** - gustavobio - hlapp - **ibartomeus** - **Ironholds** - jabard89 - jangorecki - **jarioksa** - jebyrnes - **jeroen** - **jimmyodonnell** - joelnitta - johnbaums - jonmcalder - jordancasey - **josephwb** - jsgosnell - JulietteLgls - **jwilk** - kamapu - **karthik** - **katrinleinweber** - KevCaz - kgturner - kmeverson - Koalha - **ljvillanueva** - **maelle** - Markus2015 - matutosi - mcsiple - MikkoVihtakari - millerjef - miriamgrace - mpnelsen - MUSEZOOLVERT - nate-d-olson - nmatzke - npch - ocstringham - p-neves - p-schaefer - padpadpadpad - paternogbc - **patperu** - pederengelstad - philippi - Phylloxera - **pmarchand1** - pozsgaig - pssguy - **raredd** - rec3141 - **Rekyt** - RodgerG - rossmounce - sariya - sastoudt - scelmendorf - **sckott** - SimonGoring - snsheth - snubian - Squiercg - sunray1 - **taddallas** - tdjames1 - tmkurobe - toczydlowski - tpaulson1 - tpoisot - **TrashBirdEcology** - **trvinh** - **vijaybarve** - wcornwell - willpearse - wpetry - yhg926 - **zachary-foster**

## Road map

Check out our [milestones](https://github.com/ropensci/taxize/milestones) to see what we plan to get done for each version.

## Meta

* Please [report any issues or bugs](https://github.com/ropensci/taxize/issues).
* License: MIT
* Get citation information for `taxize` in R doing `citation(package = 'taxize')`
* 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.

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

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GitHub Events

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Watch event: 13
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Pull request event: 3
Fork event: 3

Last Year

Create event: 1
Commit comment event: 1
Release event: 1
Issues event: 24
Watch event: 13
Issue comment event: 61
Push event: 44
Pull request event: 3
Fork event: 3

Committers

Last synced: 4 months ago

All Time

Total Commits: 2,176
Total Committers: 44
Avg Commits per committer: 49.455
Development Distribution Score (DDS): 0.214

Past Year

Commits: 45
Committers: 6
Avg Commits per committer: 7.5
Development Distribution Score (DDS): 0.4

Top Committers

Name	Email	Commits
Scott Chamberlain	m**s@g**m	1,710
EDiLD	s**2@u**e	192
Zachary S.L. Foster	z**9@g**m	86
edisz	e**s@g**m	33
trvinh	t**h@g**m	26
Rekyt	m**e@e**r	16
Zachary Foster	f**z@p**n	13
Bastian Greshake	b**e@g**m	12
Gaopeng Li	9**9@q**m	11
Maëlle Salmon	m**n@y**e	9
Zebulun Arendsee	a**e@i**u	7
Philippe Marchand	p**d@r**g	7
Carl Boettiger	c**g@g**m	6
Jari Oksanen	j**n@o**i	6
Karthik Ram	k**m@g**m	4
Tim	t**m@p**n	3
Brian M. Schilder	3****r	3
Jimmy O'Donnell	j**o@g**m	3
Jeroen Ooms	j**s@g**m	2
Francois Michonneau	f**u@g**m	2
fozy81	f**1@g**m	2
cob-staines	c**s@g**m	1
Salix	3****d	1
Robert Redd	r**1@g**m	1
Katrin Leinweber	k**r@t**u	1
Luis J. Villanueva	l**a@c**m	1
Maëlle Salmon	m**e@i**m	1
Timothée Poisot	t**t@u**a	1
ironholds	i**s@g**m	1
taddallas	t**s@u**u	1
and 14 more...

Committer Domains (Top 20 + Academic)

pop-os.localdomain: 2 uni-landau.de: 1 ens-lyon.fr: 1 qq.com: 1 iastate.edu: 1 rstudio01.research.sesync.org: 1 oulu.fi: 1 github.com: 1 tib.eu: 1 coquipr.com: 1 itsalocke.com: 1 uqar.ca: 1 ucdavis.edu: 1 covimo.de: 1 posteo.de: 1 jwilk.net: 1 chatterjee.net: 1 bu.edu: 1 rediffmail.com: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 747
Total pull requests: 202
Average time to close issues: 3 months
Average time to close pull requests: 3 days
Total issue authors: 194
Total pull request authors: 38
Average comments per issue: 3.64
Average comments per pull request: 0.97
Merged pull requests: 194
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 11
Pull requests: 4
Average time to close issues: about 2 months
Average time to close pull requests: about 2 hours
Issue authors: 10
Pull request authors: 2
Average comments per issue: 4.55
Average comments per pull request: 0.75
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

sckott (411)
eduardszoecs (43)
zachary-foster (15)
arendsee (8)
maelle (6)
ocstringham (6)
davharris (5)
andzandz11 (5)
vijaybarve (5)
wcornwell (4)
ahhurlbert (4)
bw4sz (4)
Alectoria (4)
azizka (3)
kgturner (3)

Pull Request Authors

eduardszoecs (97)
sckott (26)
zachary-foster (21)
trvinh (8)
gpli (5)
arendsee (4)
jarioksa (3)
fmichonneau (2)
bschilder (2)
fozy81 (2)
jimmyodonnell (2)
cob-staines (2)
Ironholds (2)
katrinleinweber (2)
pmarchand1 (2)

Top Labels

Issue Labels

bug (197) datasources (47) feature (41) get_classification (32) docs (13) question (11) fromemail (11) manuscript (10) sql (8) EOL (7) urgent (6) cran-release (6) consistent_api (5) iucn (5) tnrs (3) deprecate_defunct (3) hacktoberfest (2) good-first-issue (2) local_data (1) later (1) docker (1) os:windows (1)

Pull Request Labels

bug (2) get_classification (1) consistent_api (1) docs (1)

Packages

Total packages: 2
Total downloads: unknown

Total dependent packages: 3
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 64

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

Documentation: https://pkg.go.dev/github.com/ropensci/taxize#section-documentation
License: other
Latest release: v0.10.0
published 11 months ago

Versions: 48
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-taxize

Homepage: https://docs.ropensci.org/taxize/
License: MIT
Latest release: 0.9.100
published over 3 years ago

Versions: 16
Dependent Packages: 3
Dependent Repositories: 1

Rankings

Dependent packages count: 15.6%

Average: 19.9%

Dependent repos count: 24.2%

Last synced: 4 months ago

Dependencies

DESCRIPTION cran

R >= 3.2.1 depends
R6 * imports
ape * imports
bold >= 0.8.6 imports
cli * imports
conditionz * imports
crayon * imports
crul >= 0.7.0 imports
data.table * imports
foreach * imports
graphics * imports
jsonlite * imports
methods * imports
natserv >= 1.0.0 imports
phangorn * imports
ritis >= 0.7.6 imports
rotl >= 3.0.0 imports
rredlist * imports
stats * imports
tibble >= 1.2 imports
utils * imports
wikitaxa >= 0.3.0 imports
worrms >= 0.4.0 imports
xml2 >= 1.2.0 imports
zoo * imports
testthat * suggests
vcr * suggests
vegan * suggests

.github/workflows/revdep-check.yaml actions

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

.github/workflows/rworkflows.yml actions

neurogenomics/rworkflows master composite