ritis

An interface to the Integrated Taxonomic Information System (ITIS)

• ITIS API Docs: https://www.itis.gov/ws_description.html
• Solr service: https://www.itis.gov/solr_documentation.html
• taxize book: https://taxize.dev/
• ritis docs: https://docs.ropensci.org/ritis/

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

• "mononomial": a taxonomic name with one part, e.g, Poa
• "binomial": a taxonomic name with two parts, e.g, Poa annua
• "trinomial": a taxonomic name with three parts, e.g, Poa annua annua

Installation

Stable, CRAN version

install.packages("ritis")

Dev version

remotes::install_github("ropensci/ritis")

library("ritis")

The following are examples of some functions. There are many more avaiable.

Solr service

matches only monomials

itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{0,0}*/")
#> # A tibble: 10 x 28
#>    tsn   nameWInd nameWOInd unit1 usage credibilityRati… completenessRat…
#>    <chr> <chr>    <chr>     <chr> <chr> <chr>            <chr>           
#>  1 1427… Xenocha… Xenochae… Xeno… valid TWG standards m… complete        
#>  2 1428… Myopiti… Myopitini Myop… inva… TWG standards m… unknown         
#>  3 1428… Rhynenc… Rhynenci… Rhyn… valid TWG standards m… complete        
#>  4 1428… Urophora Urophora  Urop… valid TWG standards m… complete        
#>  5 1428… Oedaspi… Oedaspid… Oeda… inva… TWG standards m… unknown         
#>  6 1428… Aciurina Aciurina  Aciu… valid TWG standards m… complete        
#>  7 1428… Callach… Callachna Call… inva… TWG standards m… unknown         
#>  8 1428… Cecidoc… Cecidoch… Ceci… valid TWG standards m… complete        
#>  9 1428… Eurosta  Eurosta   Euro… valid TWG standards m… complete        
#> 10 1428… Peronyma Peronyma  Pero… valid TWG standards m… complete        
#> # … with 21 more variables: currencyRating <chr>, taxonAuthor <chr>,
#> #   kingdom <chr>, parentTSN <chr>, rankID <chr>, rank <chr>,
#> #   hierarchySoFar <chr>, hierarchySoFarWRanks <chr>, hierarchyTSN <chr>,
#> #   publication <chr>, otherSource <chr>, createDate <chr>, updateDate <chr>,
#> #   hierarchicalSort <chr>, `_version_` <dbl>, unacceptReason <chr>,
#> #   synonyms <chr>, synonymTSNs <chr>, acceptedTSN <chr>, comment <chr>,
#> #   expert <chr>

matches only binomials

itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{1,1}[A-Za-z0-9]*/")
#> # A tibble: 10 x 25
#>    tsn   nameWInd nameWOInd unit1 unit2 usage unacceptReason credibilityRati…
#>    <chr> <chr>    <chr>     <chr> <chr> <chr> <chr>          <chr>           
#>  1 1427… Trypeta… Trypeta … Tryp… plat… inva… original name… TWG standards m…
#>  2 1427… Xenocha… Xenochae… Xeno… aura… valid <NA>           TWG standards m…
#>  3 1428… Eutreta… Eutreta … Eutr… aura… inva… original name… TWG standards m…
#>  4 1428… Xenocha… Xenochae… Xeno… dich… valid <NA>           TWG standards m…
#>  5 1428… Rhynenc… Rhynenci… Rhyn… long… valid <NA>           TWG standards m…
#>  6 1428… Aleomyi… Aleomyia… Aleo… alpha inva… junior synonym TWG standards m…
#>  7 1428… Urophor… Urophora… Urop… acut… inva… original name… TWG standards m…
#>  8 1428… Urophor… Urophora… Urop… affi… valid <NA>           TWG standards m…
#>  9 1428… Trypeta… Trypeta … Tryp… affi… inva… original name… TWG standards m…
#> 10 1428… Urophor… Urophora… Urop… card… valid <NA>           TWG standards m…
#> # … with 17 more variables: taxonAuthor <chr>, kingdom <chr>, rankID <chr>,
#> #   rank <chr>, hierarchySoFar <chr>, hierarchySoFarWRanks <chr>,
#> #   hierarchyTSN <chr>, synonyms <chr>, synonymTSNs <chr>, publication <chr>,
#> #   otherSource <chr>, acceptedTSN <chr>, createDate <chr>, updateDate <chr>,
#> #   `_version_` <dbl>, parentTSN <chr>, hierarchicalSort <chr>

REST API

Get accepted names for a TSN

accepted_names(tsn = 504239)
#> # A tibble: 1 x 3
#>   acceptedName        acceptedTsn author    
#>   <chr>               <chr>       <chr>     
#> 1 Dasiphora fruticosa 836659      (L.) Rydb.

Get common names for a TSN

common_names(tsn = 183833)
#> # A tibble: 3 x 3
#>   commonName          language tsn   
#>   <chr>               <chr>    <chr> 
#> 1 African hunting dog English  183833
#> 2 African Wild Dog    English  183833
#> 3 Painted Hunting Dog English  183833

Full hierarchy for a TSN

hierarchy_full(tsn = 37906)
#> # A tibble: 60 x 5
#>    parentname        parenttsn rankname      taxonname       tsn   
#>    <chr>             <chr>     <chr>         <chr>           <chr> 
#>  1 ""                ""        Kingdom       Plantae         202422
#>  2 "Plantae"         "202422"  Subkingdom    Viridiplantae   954898
#>  3 "Viridiplantae"   "954898"  Infrakingdom  Streptophyta    846494
#>  4 "Streptophyta"    "846494"  Superdivision Embryophyta     954900
#>  5 "Embryophyta"     "954900"  Division      Tracheophyta    846496
#>  6 "Tracheophyta"    "846496"  Subdivision   Spermatophytina 846504
#>  7 "Spermatophytina" "846504"  Class         Magnoliopsida   18063 
#>  8 "Magnoliopsida"   "18063"   Superorder    Asteranae       846535
#>  9 "Asteranae"       "846535"  Order         Asterales       35419 
#> 10 "Asterales"       "35419"   Family        Asteraceae      35420 
#> # … with 50 more rows

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for ritis in R doing citation(package = 'ritis')
• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.