This article is about taxonomy in R.
If you have any comments or suggestions for additions or improvements
for this article submit an
issue , or make some
changes and submit a pull
request . 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 access to 20ish sources of
taxonomic data sources. This is the place to go for most taxononomic
data. taxize 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.
-
taxizedb came out of the
taxize package, with sights set on
helping people work with larger taxonomic data sets, or that perhaps
have infrequent access to the internet.
taxizedb 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 is starting
to gain some of the functionality of
taxize (e.g., get a taxonomic
classification) but without having to do web requests, and doing
large set of them much faster.
-
ritis 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 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 client for the WoRMS (World
Register of Marine Species) API.
Contains mostly taxonomic data, but also trait data.
-
Taxonstand 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 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 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 is a thin client for
the Go based library gnparser
from the GlobalNamesArchitecture project, which uses a Parsing
Expression Grammar (PEG) to parse taxonomic names very quickly.
-
metacoder specializes in
metabarcoding. It can parse, manipulate, and visualize
metabarcoding/taxonomic data. It leverages the
taxa package (
GitHub )
-
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 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 - match species list
against a reference list. Still in development
NCBI data
- NCBI taxonomic data is available from a number of R packages.
taxizedb provides access to local
version of NCBI’s taxonomy - in addition to taxonomies for other
data sources (see above). ncbit
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 contains functions
for assigning taxonomy to NCBI accession numbers and taxon IDs based
on NCBI’s accession2taxid
and taxdump
files.
-
microclass has functions for
assigning 16S sequence data to a taxonomic level in the tree-of-life
for prokaryotes.
Specialized packages
-
monographaR functions to
facilitate the production of plant taxonomic monographs
-
taxlist has functions to import
species lists from
Turboveg , a database
management system for vegetation data
-
vegdata has functions to get
taxonomic data from
Turboveg , and
VegetWeb (German plant data)