rtaxref

:package: R client to the API of French Taxonomical Reference (TAXREF)

https://github.com/rekyt/rtaxref

Science Score: 26.0%

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
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (21.4%) to scientific vocabulary

Keywords

api api-client api-wrapper biodiversity r r-package rstats taxonomy

Last synced: 4 months ago · JSON representation

Repository

:package: R client to the API of French Taxonomical Reference (TAXREF)

Basic Info

Host: GitHub
Owner: Rekyt
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://rekyt.github.io/rtaxref/
Size: 3.76 MB

Statistics

Stars: 5
Watchers: 1
Forks: 1
Open Issues: 18
Releases: 0

Topics

api api-client api-wrapper biodiversity r r-package rstats taxonomy

Created almost 7 years ago · Last pushed over 3 years ago

Metadata Files

Readme License Code of conduct Citation Codemeta

README.Rmd

---
output: github_document
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%",
  eval = TRUE
)
```

# rtaxref  an R client to the French Taxonomical Reference


[![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)
[![codecov](https://codecov.io/gh/Rekyt/rtaxref/branch/master/graph/badge.svg)](https://codecov.io/gh/Rekyt/rtaxref)
[![R-CMD-check](https://github.com/Rekyt/rtaxref/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Rekyt/rtaxref/actions/workflows/R-CMD-check.yaml)
  

The goal of rtaxref is to provide an R client to TAXREF API,
the French Taxonomical Reference and associated database on species.
The API provides nomenclature, taxonomy, biogeographic repartition, statuses
and interactions of species. See the API documentation
[here](https://taxref.mnhn.fr/taxref-web/api/doc).

This project is still under development (especially the documentation) but most
functions should work out of the box. Please do use the
[issue tracker](https://github.com/Rekyt/rtaxref/issues) for any bug report,
suggestion, or idea.

## Installation

`rtaxref` is not yet on CRAN. However, you can install the development version of `rtaxref` from GitHub with:

```{r, eval=FALSE}
# install.packages("remotes")
remotes::install_github("Rekyt/rtaxref")
```


## Citation

`rtaxref` contains functions to retrieve data from TAXREF-Hub. The access data is released under the [Creative Commons Attribution-ShareAlike 3.0 (CC BY-SA 3.0) license](https://creativecommons.org/licenses/by-sa/3.0/). A suggestion of citation is included in `rtaxref` via `citation("rtaxref")`.

```{r citation}
citation("rtaxref")
```

## Usage

To avoid collisions with other packages all `rtaxref` functions are prefixed with `rt_*()`, for example `rt_taxa_id()` lets you access to the information about a taxon using its unique id (also called `cdNom` in TAXREF):

```{r rt_taxa_id}
library("rtaxref")

rt_taxa_id(id = 101027)
```

You get information about the taxon related to taxonomy, the referance name, vernacular names as well as distribution information.

`rt_taxa_search()` let's you search a taxon with different criteria:

```{r rt_taxa_search}
rt_taxa_search(sciname = "Helianthus annuus")
```

You a full list of functions included in `rtaxref` by going to the [`rtaxref` website](https://rekyt.github.io/rtaxref).


## Code of Conduct

Please note that the 'rtaxref' project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.

## Related projects

Other packages lets you work with taxonomical information from relevant databases:

- [`taxize`](https://github.com/ropensci/taxize) let's you work with many databases as well as clean a list of taxon names,
- [`ritis`](https://github.com/ropensci/ritis) a client for another taxonomic database,
- [`taxa`](https://github.com/ropensci/taxa) a package that proposes a reference class for taxonomic information (maybe used by `rtaxref` in the future),
- [CRAN taxonomy Task View](https://github.com/ropensci/taxonomy) references many related packages that are used to work with taxonomic information.

Owner

Name: Matthias Grenié
Login: Rekyt
Kind: user
Location: Grenoble, France
Company: Université Grenoble Alpes / Laboratoire d'Écologie Alpine (LECA)

Website: http://rekyt.github.io/
Repositories: 61
Profile: https://github.com/Rekyt

Assistant Professor of Biostatistics & Ecology

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "rtaxref",
  "description": "Provides an R client to the TaxRef API <https://taxref.mnhn.fr/taxref-web/api/doc>, the French Taxonomical Reference Database which indexes names of species with unique identifiers as well as conservation statuses, biological interactions and taxonomic relationships.",
  "name": "rtaxref: An R client for TaxRef the French Taxonomical Database",
  "codeRepository": "https://github.com/Rekyt/rtaxref",
  "issueTracker": "https://github.com/Rekyt/rtaxref/issues",
  "license": "https://spdx.org/licenses/GPL-3.0",
  "version": "0.1.0",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.2.0 (2022-04-22 ucrt)",
  "author": [
    {
      "@type": "Person",
      "givenName": "Matthias",
      "familyName": "Greni",
      "email": "matthias.grenie@gmail.com",
      "@id": "https://orcid.org/0000-0002-4659-7522"
    },
    {
      "@type": "Person",
      "givenName": "Hugo",
      "familyName": "Gruson",
      "@id": "https://orcid.org/0000-0002-4094-1476"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Matthias",
      "familyName": "Greni",
      "email": "matthias.grenie@gmail.com",
      "@id": "https://orcid.org/0000-0002-4659-7522"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "knitr",
      "name": "knitr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=knitr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "vcr",
      "name": "vcr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=vcr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rmarkdown",
      "name": "rmarkdown",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
    }
  ],
  "softwareRequirements": {
    "1": {
      "@type": "SoftwareApplication",
      "identifier": "httr",
      "name": "httr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=httr"
    },
    "2": {
      "@type": "SoftwareApplication",
      "identifier": "tibble",
      "name": "tibble",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tibble"
    },
    "SystemRequirements": null
  },
  "fileSize": "973.219KB",
  "citation": [
    {
      "@type": "SoftwareSourceCode",
      "author": [
        {
          "@type": "Person",
          "givenName": "Matthias",
          "familyName": "Greni"
        },
        {
          "@type": "Person",
          "givenName": "Hugo",
          "familyName": "Gruson"
        }
      ],
      "name": "{rtaxref}: An {R} Client for {TAXREF} the French Taxonomical Reference {API}",
      "url": "https://github.com/Rekyt/rtaxref",
      "description": "R package version 0.1.0"
    },
    {
      "@type": "CreativeWork",
      "datePublished": "2022",
      "author": [
        {
          "@type": "Organization",
          "name": "TAXTREF"
        }
      ],
      "url": "https://taxref.mnhn.fr/taxref-web/accueil",
      "description": "Data released under the Creative Commons Attribution-ShareAlike 3.0 (CC BY-SA 3.0) license"
    }
  ],
  "readme": "https://github.com/Rekyt/rtaxref/blob/main/README.md",
  "contIntegration": [
    "https://codecov.io/gh/Rekyt/rtaxref",
    "https://github.com/Rekyt/rtaxref/actions/workflows/R-CMD-check.yaml"
  ],
  "developmentStatus": "https://www.repostatus.org/#active",
  "keywords": [
    "api",
    "api-client",
    "api-wrapper",
    "biodiversity",
    "r",
    "r-package",
    "rstats",
    "taxonomy"
  ]
}

GitHub Events

Total

Watch event: 2

Last Year

Watch event: 2

Committers

Last synced: almost 2 years ago

All Time

Total Commits: 95
Total Committers: 2
Avg Commits per committer: 47.5
Development Distribution Score (DDS): 0.011

Past Year

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

Top Committers

Name	Email	Commits
Rekyt	m**e@e**r	94
Hugo Gruson	h**n@p**m	1

Committer Domains (Top 20 + Academic)

ens-lyon.fr: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time

Total issues: 32
Total pull requests: 7
Average time to close issues: 6 months
Average time to close pull requests: 1 day
Total issue authors: 4
Total pull request authors: 1
Average comments per issue: 0.47
Average comments per pull request: 0.86
Merged pull requests: 7
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 5
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
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

Rekyt (28)
Bisaloo (1)
PascalIrz (1)
sPuechmailleGitHub (1)

Pull Request Authors

Rekyt (7)

Top Labels

Issue Labels

enhancement (13) bug (6) Contact API maintainer (2)

Pull Request Labels

Dependencies

DESCRIPTION cran

httr * imports
tibble * imports
knitr * suggests
rmarkdown * suggests
testthat * suggests
vcr * suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

rtaxref

Science Score: 26.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies