ritis

Project Status: Active – The project has reached a stable, usable state and is being actively developed. cran checks Build Status Build status codecov rstudio mirror downloads cran version

An interface to the Integrated Taxonomic Information System (ITIS)

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

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

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