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.

The taxize tutorial is can be found at http://ropensci.org/tutorials/taxize_tutorial.html

Contributors

• Scott Chamberlain
• Eduard Szöcs
• Carl Boettiger
• Karthik Ram
• Ignasi Bartomeus
• John Baumgartner

The functions in the package that hit a specific API have a prefix and suffix separated by an underscore. They follow the format of service_whatitdoes. For example, gnr_resolve uses the Global Names Resolver API to resolve species names. General functions in the package that don't hit a specific API don't have two words separated by an underscore, e.g., classification.

You need API keys for Encyclopedia of Life (EOL), the Universal Biological Indexer and Organizer (uBio), Tropicos, and Plantminer.

The following are URL's for API documentation, where to get API keys, and what prefix they have in function names.

Currently implemented in taxize

Souce	Function prefix	API Docs	API key
Encylopedia of Life	eol	link	link
Taxonomic Name Resolution Service	tnrs	link	none
Integrated Taxonomic Information Service	itis	link	none
Phylomatic	phylomatic	link	none
uBio	ubio	link	link
Global Names Resolver	gnr	link	none
Global Names Index	gni	link	none
IUCN Red List	iucn	link	none
Tropicos	tp	link	link
Plantminer	plantminer	link	link
Theplantlist dot org	tpl	**	none
Catalogue of Life	col	link	none
Global Invasive Species Database	gisd	***	none
National Center for Biotechnology Information	ncbi	none	none
CANADENSYS Vascan name search API	vascan	link	none
International Plant Names Index (IPNI)	ipni	link	none
World Register of Marine Species (WoRMS)	worms	link	none

**: There are none! We suggest using TPL and TPLck functions in the taxonstand package. We provide two functions to get bullk data: tpl_families and tpl_get.

***: There are none! The function scrapes the web directly.

May be in taxize in the future...

• USDA Plants
• NatureServe
• Lichen Taxon dictionary
• MycoBank

Quickstart

Install taxize

• Stable version from CRAN:

install.packages("taxize")
library(taxize)

• Or, development version from GitHub:

You'll need XMLSchema and SSSOAP

download.file("http://www.omegahat.org/Prerelease/XMLSchema_0.8-0.tar.gz", "XMLSchema")
install.packages("XMLSchema", type="source", repos = NULL)
download.file("http://www.omegahat.org/Prerelease/SSOAP_0.91-0.tar.gz", "SSOAP")
install.packages("SSOAP", type="source", repos = NULL)

install.packages("devtools")
library(devtools)
install_github("taxize", "ropensci", ref="worms")
library(taxize)

A few examples (for more click here)

Get unique taxonomic identifier from NCBI

uids <- get_uid(c("Chironomus riparius", "Chaetopteryx"))

And retrieve classification

out <- classification(uids)
lapply(out, head)

[[1]]
                name         rank
1 cellular organisms      no rank
2          Eukaryota superkingdom
3       Opisthokonta      no rank
4            Metazoa      kingdom
5          Eumetazoa      no rank
6          Bilateria      no rank

[[2]]
                name         rank
1 cellular organisms      no rank
2          Eukaryota superkingdom
3       Opisthokonta      no rank
4            Metazoa      kingdom
5          Eumetazoa      no rank
6          Bilateria      no rank

Make a phylogeny from Phylomatic

Input the taxonomic names

taxa <- c("Poa annua", "Phlox diffusa", "Helianthus annuus")

Fetch the tree - the formatting of names and higher taxonmy is done within the function

tree <- phylomatic_tree(taxa=taxa, storedtree = "R20120829")

Plot

plot(tree)

Meta

Please report any issues or bugs.

License: MIT

This package is part of the rOpenSci project.

To cite package taxize in publications use:

To cite taxize in publications use:

  Scott Chamberlain and Eduard Szocs (2013). taxize - taxonomic search
  and retrieval in R. F1000Research, 2:191. URL:
  http://f1000research.com/articles/2-191/v2.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {taxize - taxonomic search and retrieval in R},
    journal = {F1000Research},
    author = {{Scott Chamberlain} and {Eduard Szocs}},
    year = {2013},
    url = {http://f1000research.com/articles/2-191/v2},
  }

Get citation information for taxize in R doing citation(package = 'taxize')