ritis introduction

Scott Chamberlain

2020-04-17

An interface to the Integrated Taxonomic Information System (ITIS)

See also the taxize book (https://taxize.dev/) for a manual on working with taxonomic data in R, including with ITIS data.

How to cite ITIS. From https://itis.gov/citation.html

To cite data obtained from ITIS, the following citation format is offered as a suggestion:

Retrieved [month, day, year], from the Integrated Taxonomic Information System on-line database, http://www.itis.gov.

ITIS is one of many different taxonomic data sources. Other include: Catalogue of Life (and COL+), NCBI taxonomy, International Plant Names Index, Index Fungorum, and more. The Wikipedia entry (https://en.wikipedia.org/wiki/Integrated_Taxonomic_Information_System) states that ITIS has a North American focus, but includes many taxa not in North America.

Terminology

Installation

Install from CRAN

install.packages("ritis")

Or install the development version from GitHub

remotes::install_github("ropensci/ritis")

Load ritis

library("ritis")

ITIS Solr interface

There are four methods.

These four methods use the equivalent functions in the package solrium, e.g., ritis::itis_search() uses solrium::solr_search(), etc. The itis_*() functions simply use ... to allow users to pass on parameters to the wrapped solrium functions. So do read the solrium docs.

ITIS Solr API docs: https://www.itis.gov/solr_documentation.html

Some examples:

matches only monomials

itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{0,0}*/")

matches only binomials

itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{1,1}[A-Za-z0-9]*/")

The syntax for itis_search() can be a bit hard to grasp. See this ITIS page https://itis.gov/solr_examples.html for help on generating the syntax they want for specific searches.

ITIS REST API interface

ITIS REST API docs: http://www.itis.gov/ws_description.html

The following are some example uses. There are many more methods not shown below

Get accepted names for a TSN

accepted_names(tsn = 504239)

Get common names for a TSN

common_names(tsn = 183833)

Full hierarchy for a TSN

hierarchy_full(tsn = 37906)