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https://github.com/ropensci/taxonomy

taxonomy R packages
https://github.com/ropensci/taxonomy

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taxonomy R packages

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README 

          
## Taxonomy






This article is about taxonomy in R.



If you have any comments or suggestions for additions or improvements

for this article [submit an

issue](https://github.com/ropensci/taxonomy/issues) , or make some

changes and [submit a pull

request](https://github.com/ropensci/taxonomy/pulls) . If you have an

issue with one of the packages discussed below, please contact the

maintainer of that package.



## Taxonomic Data



The following packages mostly deal with getting taxonomic data from the

web onto your machine.



  - [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) access to 20ish sources of

    taxonomic data sources. This is the place to go for most taxononomic

    data. [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) connects to a lot of

    data sources, and has consistent data outputs across the data

    sources. In addition, there’s operations that a user wants to do

    that are consistent across data sources, hiding the gory details of

    each data source. The only caveat is that if you have a really slow

    internet connection or you are dealing with A LOT of names, then you

    may want to use [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html).

  - [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html) came out of the

    [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) package, with sights set on

    helping people work with larger taxonomic data sets, or that perhaps

    have infrequent access to the internet.

    [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html) downloads taxonomic

    database dumps from many different providers - and makes it easy to

    either query them with SQL or plug into `dplyr` package to use that

    interface. [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html) is starting

    to gain some of the functionality of

    [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) (e.g., get a taxonomic

    classification) but without having to do web requests, and doing

    large set of them much faster.

  - [ritis](https://cran.rstudio.com/web/packages/ritis/index.html) is a client for the Integrated

    Taxonomic Information System (ITIS) database of taxonomic data. ITIS

    is run by USGS in the US. It provides access to ITIS’s Solr web

    service (think for search), as well as their REST API more for

    fetching data for specific things by name or taxonomic ID.

  - [wikitaxa](https://cran.rstudio.com/web/packages/wikitaxa/index.html) is a client for

    Wikipedia, Wikicommons, Wikspecies, and Wikidata taxonomic data. It

    is sometimes a bit odd since there is no interface specifically for

    taxonomic data besides Wikispecies, so you can end up with results

    that are not really taxonomic as well - but we do our best.

  - [worrms](https://cran.rstudio.com/web/packages/worrms/index.html) client for the [WoRMS (World

    Register of Marine Species)](http://www.marinespecies.org/) API.

    Contains mostly taxonomic data, but also trait data.

  - [Taxonstand](https://cran.rstudio.com/web/packages/Taxonstand/index.html) data from The Plant

    List. This package takes in plant taxon names, and downloads CSV

    files from The Plant List website, then presents those as a

    data.frame within R.



## Taxonomic Classes



The [taxa](https://cran.rstudio.com/web/packages/taxa/index.html) package defines a set of

taxonomic objects (using S3 and R6) for both use cases where only

taxonomic data is of interest, as well as when one has taxonomic data

combined with other data on the taxa.

[taxa](https://cran.rstudio.com/web/packages/taxa/index.html) aims to form the basis upon which

other taxonomic packages can be built, using common classes.



## Manipulating/Parsing Taxonomic Names



The following packages don’t fetch taxonomic dat as those in the above

section, but are focused around providing tooling around taxonomic names

and data.



  - [rgnparser](https://cran.rstudio.com/web/packages/rgnparser/index.html) is a thin client for

    the Go based library [gnparser](https://gitlab.com/gogna/gnparser)

    from the GlobalNamesArchitecture project, which uses a Parsing

    Expression Grammar (PEG) to parse taxonomic names very quickly.

  - [metacoder](https://cran.rstudio.com/web/packages/metacoder/index.html) specializes in

    metabarcoding. It can parse, manipulate, and visualize

    metabarcoding/taxonomic data. It leverages the

    [taxa](https://cran.rstudio.com/web/packages/taxa/index.html) package (

    [GitHub](https://github.com/grunwaldlab/metacoder) )

  - [taxview](https://github.com/ropensci/taxview) is a in development

    package to help users summarize taxonomic data. Summarizing so far

    is taking form of getting taxonomic hierarchy data (via the

    [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) package) to facilitate

    taxonomic summaries. Visualization isn’t done yet.



## Handling Taxonomic Name Lists



There are a few packages that deal specifically with handling species

lists:



  - [splister](https://github.com/sckott/splister) - match species list

    against a reference list. Still in development



## NCBI data



  - NCBI taxonomic data is available from a number of R packages.

    [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html) provides access to local

    version of NCBI’s taxonomy - in addition to taxonomies for other

    data sources (see above). [ncbit](https://cran.rstudio.com/web/packages/ncbit/index.html)

    makes NCBI taxonomic data locally available and searchable as an R

    object (a `data.frame`). The package comes with a version from 2013,

    but you can choose to update it; although updating it still seemed

    to use the old version from 2013.

    [taxonomizr](https://cran.rstudio.com/web/packages/taxonomizr/index.html) contains functions

    for assigning taxonomy to NCBI accession numbers and taxon IDs based

    on NCBI’s `accession2taxid` and `taxdump` files.

  - [microclass](https://cran.rstudio.com/web/packages/microclass/index.html) has functions for

    assigning 16S sequence data to a taxonomic level in the tree-of-life

    for prokaryotes.



## Specialized packages



  - [monographaR](https://cran.rstudio.com/web/packages/monographaR/index.html) functions to

    facilitate the production of plant taxonomic monographs

  - [taxlist](https://cran.rstudio.com/web/packages/taxlist/index.html) has functions to import

    species lists from

    [Turboveg](https://www.synbiosys.alterra.nl/turboveg/) , a database

    management system for vegetation data

  - [vegdata](https://cran.rstudio.com/web/packages/vegdata/index.html) has functions to get

    taxonomic data from

    [Turboveg](https://www.synbiosys.alterra.nl/turboveg/) , and

    [VegetWeb](https://www.vegetweb.de/) (German plant data)






### CRAN packages:



  - [metacoder](https://cran.rstudio.com/web/packages/metacoder/index.html)

  - [microclass](https://cran.rstudio.com/web/packages/microclass/index.html)

  - [monographaR](https://cran.rstudio.com/web/packages/monographaR/index.html)

  - [ncbit](https://cran.rstudio.com/web/packages/ncbit/index.html)

  - [rgnparser](https://cran.rstudio.com/web/packages/rgnparser/index.html)

  - [ritis](https://cran.rstudio.com/web/packages/ritis/index.html)

  - [taxa](https://cran.rstudio.com/web/packages/taxa/index.html) (core)

  - [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) (core)

  - [taxizedb](https://cran.rstudio.com/web/packages/taxizedb/index.html)

  - [taxlist](https://cran.rstudio.com/web/packages/taxlist/index.html)

  - [taxonomizr](https://cran.rstudio.com/web/packages/taxonomizr/index.html)

  - [Taxonstand](https://cran.rstudio.com/web/packages/Taxonstand/index.html)

  - [vegdata](https://cran.rstudio.com/web/packages/vegdata/index.html)

  - [wikitaxa](https://cran.rstudio.com/web/packages/wikitaxa/index.html)

  - [worrms](https://cran.rstudio.com/web/packages/worrms/index.html)



### Related links:



  - [Phylogenetics Task

    View](https://cran.rstudio.com/web/views/Phylogenetics.html)