{"id":13707698,"url":"https://github.com/ropensci/taxonomy","last_synced_at":"2025-12-27T10:55:45.579Z","repository":{"id":136421645,"uuid":"105911337","full_name":"ropensci/taxonomy","owner":"ropensci","description":"taxonomy R packages","archived":false,"fork":false,"pushed_at":"2024-04-16T12:34:18.000Z","size":32,"stargazers_count":43,"open_issues_count":6,"forks_count":4,"subscribers_count":5,"default_branch":"main","last_synced_at":"2024-11-13T16:42:13.970Z","etag":null,"topics":["cran","r","ropensci","task-view","taxonomy"],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ropensci.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-10-05T16:06:19.000Z","updated_at":"2024-10-28T22:32:25.000Z","dependencies_parsed_at":null,"dependency_job_id":"646829f9-4055-41a6-b042-524e40c864d9","html_url":"https://github.com/ropensci/taxonomy","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ropensci%2Ftaxonomy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ropensci%2Ftaxonomy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ropensci%2Ftaxonomy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ropensci%2Ftaxonomy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ropensci","download_url":"https://codeload.github.com/ropensci/taxonomy/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252617092,"owners_count":21777129,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cran","r","ropensci","task-view","taxonomy"],"created_at":"2024-08-02T22:01:40.274Z","updated_at":"2025-12-27T10:55:45.566Z","avatar_url":"https://github.com/ropensci.png","language":"HTML","funding_links":[],"categories":["HTML"],"sub_categories":[],"readme":"## Taxonomy\n\n\u003cdiv\u003e\n\nThis article is about taxonomy in R.\n\nIf you have any comments or suggestions for additions or improvements\nfor this article [submit an\nissue](https://github.com/ropensci/taxonomy/issues) , or make some\nchanges and [submit a pull\nrequest](https://github.com/ropensci/taxonomy/pulls) . If you have an\nissue with one of the packages discussed below, please contact the\nmaintainer of that package.\n\n## Taxonomic Data\n\nThe following packages mostly deal with getting taxonomic data from the\nweb onto your machine.\n\n  - [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) access to 20ish sources of\n    taxonomic data sources. This is the place to go for most taxononomic\n    data. [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) connects to a lot of\n    data sources, and has consistent data outputs across the data\n    sources. In addition, there’s operations that a user wants to do\n    that are consistent across data sources, hiding the gory details of\n    each data source. The only caveat is that if you have a really slow\n    internet connection or you are dealing with A LOT of names, then you\n    may want to use [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html).\n  - [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html) came out of the\n    [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) package, with sights set on\n    helping people work with larger taxonomic data sets, or that perhaps\n    have infrequent access to the internet.\n    [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html) downloads taxonomic\n    database dumps from many different providers - and makes it easy to\n    either query them with SQL or plug into `dplyr` package to use that\n    interface. [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html) is starting\n    to gain some of the functionality of\n    [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) (e.g., get a taxonomic\n    classification) but without having to do web requests, and doing\n    large set of them much faster.\n  - [ritis](https://cran.rstudio.com/web/packages/ritis/index.html) is a client for the Integrated\n    Taxonomic Information System (ITIS) database of taxonomic data. ITIS\n    is run by USGS in the US. It provides access to ITIS’s Solr web\n    service (think for search), as well as their REST API more for\n    fetching data for specific things by name or taxonomic ID.\n  - [wikitaxa](https://cran.rstudio.com/web/packages/wikitaxa/index.html) is a client for\n    Wikipedia, Wikicommons, Wikspecies, and Wikidata taxonomic data. It\n    is sometimes a bit odd since there is no interface specifically for\n    taxonomic data besides Wikispecies, so you can end up with results\n    that are not really taxonomic as well - but we do our best.\n  - [worrms](https://cran.rstudio.com/web/packages/worrms/index.html) client for the [WoRMS (World\n    Register of Marine Species)](http://www.marinespecies.org/) API.\n    Contains mostly taxonomic data, but also trait data.\n  - [Taxonstand](https://cran.rstudio.com/web/packages/Taxonstand/index.html) data from The Plant\n    List. This package takes in plant taxon names, and downloads CSV\n    files from The Plant List website, then presents those as a\n    data.frame within R.\n\n## Taxonomic Classes\n\nThe [taxa](https://cran.rstudio.com/web/packages/taxa/index.html) package defines a set of\ntaxonomic objects (using S3 and R6) for both use cases where only\ntaxonomic data is of interest, as well as when one has taxonomic data\ncombined with other data on the taxa.\n[taxa](https://cran.rstudio.com/web/packages/taxa/index.html) aims to form the basis upon which\nother taxonomic packages can be built, using common classes.\n\n## Manipulating/Parsing Taxonomic Names\n\nThe following packages don’t fetch taxonomic dat as those in the above\nsection, but are focused around providing tooling around taxonomic names\nand data.\n\n  - [rgnparser](https://cran.rstudio.com/web/packages/rgnparser/index.html) is a thin client for\n    the Go based library [gnparser](https://gitlab.com/gogna/gnparser)\n    from the GlobalNamesArchitecture project, which uses a Parsing\n    Expression Grammar (PEG) to parse taxonomic names very quickly.\n  - [metacoder](https://cran.rstudio.com/web/packages/metacoder/index.html) specializes in\n    metabarcoding. It can parse, manipulate, and visualize\n    metabarcoding/taxonomic data. It leverages the\n    [taxa](https://cran.rstudio.com/web/packages/taxa/index.html) package (\n    [GitHub](https://github.com/grunwaldlab/metacoder) )\n  - [taxview](https://github.com/ropensci/taxview) is a in development\n    package to help users summarize taxonomic data. Summarizing so far\n    is taking form of getting taxonomic hierarchy data (via the\n    [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) package) to facilitate\n    taxonomic summaries. Visualization isn’t done yet.\n\n## Handling Taxonomic Name Lists\n\nThere are a few packages that deal specifically with handling species\nlists:\n\n  - [splister](https://github.com/sckott/splister) - match species list\n    against a reference list. Still in development\n\n## NCBI data\n\n  - NCBI taxonomic data is available from a number of R packages.\n    [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html) provides access to local\n    version of NCBI’s taxonomy - in addition to taxonomies for other\n    data sources (see above). [ncbit](https://cran.rstudio.com/web/packages/ncbit/index.html)\n    makes NCBI taxonomic data locally available and searchable as an R\n    object (a `data.frame`). The package comes with a version from 2013,\n    but you can choose to update it; although updating it still seemed\n    to use the old version from 2013.\n    [taxonomizr](https://cran.rstudio.com/web/packages/taxonomizr/index.html) contains functions\n    for assigning taxonomy to NCBI accession numbers and taxon IDs based\n    on NCBI’s `accession2taxid` and `taxdump` files.\n  - [microclass](https://cran.rstudio.com/web/packages/microclass/index.html) has functions for\n    assigning 16S sequence data to a taxonomic level in the tree-of-life\n    for prokaryotes.\n\n## Specialized packages\n\n  - [monographaR](https://cran.rstudio.com/web/packages/monographaR/index.html) functions to\n    facilitate the production of plant taxonomic monographs\n  - [taxlist](https://cran.rstudio.com/web/packages/taxlist/index.html) has functions to import\n    species lists from\n    [Turboveg](https://www.synbiosys.alterra.nl/turboveg/) , a database\n    management system for vegetation data\n  - [vegdata](https://cran.rstudio.com/web/packages/vegdata/index.html) has functions to get\n    taxonomic data from\n    [Turboveg](https://www.synbiosys.alterra.nl/turboveg/) , and\n    [VegetWeb](https://www.vegetweb.de/) (German plant data)\n\n\u003c/div\u003e\n\n### CRAN packages:\n\n  - [metacoder](https://cran.rstudio.com/web/packages/metacoder/index.html)\n  - [microclass](https://cran.rstudio.com/web/packages/microclass/index.html)\n  - [monographaR](https://cran.rstudio.com/web/packages/monographaR/index.html)\n  - [ncbit](https://cran.rstudio.com/web/packages/ncbit/index.html)\n  - [rgnparser](https://cran.rstudio.com/web/packages/rgnparser/index.html)\n  - [ritis](https://cran.rstudio.com/web/packages/ritis/index.html)\n  - [taxa](https://cran.rstudio.com/web/packages/taxa/index.html) (core)\n  - [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) (core)\n  - [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html)\n  - [taxlist](https://cran.rstudio.com/web/packages/taxlist/index.html)\n  - [taxonomizr](https://cran.rstudio.com/web/packages/taxonomizr/index.html)\n  - [Taxonstand](https://cran.rstudio.com/web/packages/Taxonstand/index.html)\n  - [vegdata](https://cran.rstudio.com/web/packages/vegdata/index.html)\n  - [wikitaxa](https://cran.rstudio.com/web/packages/wikitaxa/index.html)\n  - [worrms](https://cran.rstudio.com/web/packages/worrms/index.html)\n\n### Related links:\n\n  - [Phylogenetics Task\n    View](https://cran.rstudio.com/web/views/Phylogenetics.html)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fropensci%2Ftaxonomy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fropensci%2Ftaxonomy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fropensci%2Ftaxonomy/lists"}