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)

Package API

Installation

Stable, CRAN version

install.packages("ritis")

Dev version

devtools::install_github("ropensci/ritis")
library("ritis")

Solr service

matches only monomials

itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{0,0}*/")
#> # A tibble: 10 x 20
#>    tsn   nameWInd nameWOInd unit1 usage credibilityRati… completenessRat…
#>    <chr> <chr>    <chr>     <chr> <chr> <chr>            <chr>           
#>  1 1348… Phthiri… Phthirii… Phth… valid No review; untr… unknown         
#>  2 1348… Phthiria Phthiria  Phth… valid No review; untr… unknown         
#>  3 1348… Poecilo… Poecilog… Poec… valid No review; untr… unknown         
#>  4 1348… Neacreo… Neacreot… Neac… valid No review; untr… unknown         
#>  5 1348… Geronin… Geroninae Gero… valid No review; untr… unknown         
#>  6 1348… Geron    Geron     Geron valid No review; untr… unknown         
#>  7 1349… Cythere… Cytherei… Cyth… valid No review; untr… unknown         
#>  8 1349… Pantarb… Pantarbes Pant… valid No review; untr… unknown         
#>  9 1349… Tomomyz… Tomomyzi… Tomo… valid No review; untr… unknown         
#> 10 1349… Amphico… Amphicos… Amph… valid No review; untr… unknown         
#> # … with 13 more variables: currencyRating <chr>, kingdom <chr>,
#> #   parentTSN <chr>, rankID <chr>, rank <chr>, hierarchySoFar <chr>,
#> #   hierarchySoFarWRanks <chr>, hierarchyTSN <chr>, otherSource <chr>,
#> #   createDate <chr>, updateDate <chr>, hierarchicalSort <chr>,
#> #   `_version_` <dbl>

matches only binomials

itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{1,1}[A-Za-z0-9]*/")
#> # A tibble: 10 x 24
#>    tsn   nameWInd nameWOInd unit1 unit2 usage unacceptReason
#>    <chr> <chr>    <chr>     <chr> <chr> <chr> <chr>         
#>  1 1347… Rhabdop… Rhabdops… Rhab… mus   inva… junior synonym
#>  2 1347… Apolysi… Apolysis… Apol… neut… valid <NA>          
#>  3 1347… Pseudog… Pseudoge… Pseu… neut… inva… junior synonym
#>  4 1347… Apolysi… Apolysis… Apol… nigr… valid <NA>          
#>  5 1347… Oligodr… Oligodra… Olig… nigr… inva… junior synonym
#>  6 1347… Apolysi… Apolysis… Apol… obsc… valid <NA>          
#>  7 1347… Pseudog… Pseudoge… Pseu… obsc… inva… junior synonym
#>  8 1347… Apolysi… Apolysis… Apol… palp… valid <NA>          
#>  9 1347… Oligodr… Oligodra… Olig… palp… inva… junior synonym
#> 10 1347… Apolysi… Apolysis… Apol… pann… valid <NA>          
#> # … with 17 more variables: credibilityRating <chr>, taxonAuthor <chr>,
#> #   kingdom <chr>, rankID <chr>, rank <chr>, hierarchySoFar <chr>,
#> #   hierarchySoFarWRanks <chr>, hierarchyTSN <chr>, synonyms <chr>,
#> #   synonymTSNs <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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