ritis introduction

Scott Chamberlain

2019-10-28

An interface to the Integrated Taxonomic Information System (ITIS)

See also the taxize book for a manual on working with taxonomic data in R, including with ITIS data.

Installation

Install from CRAN

install.packages("ritis")

Or install the development version from GitHub

devtools::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]*/")

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)