rOpenSci: The ritis package

An interface to the Integrated Taxonomic Information System (ITIS)

• ITIS API Docs
• Solr service
• taxize book

Package API

• accepted_names
• any_match_count
• comment_detail
• common_names
• core_metadata
• coverage
• credibility_rating
• credibility_ratings
• currency
• date_data
• description
• experts
• full_record
• geographic_divisions
• geographic_values
• global_species_completeness
• hierarchy_down
• hierarchy_full
• hierarchy_up
• itis_facet
• itis_group
• itis_highlight
• itis_search
• jurisdiction_origin_values
• jurisdiction_values
• jurisdictional_origin
• kingdom_name
• kingdom_names
• last_change_date
• lsid2tsn
• other_sources
• parent_tsn
• publications
• rank_name
• rank_names
• record
• review_year
• scientific_name
• search_any_match_paged
• search_anymatch
• search_common
• search_scientific
• synonym_names
• taxon_authorship
• terms
• tsn_by_vernacular_language
• tsn2lsid
• unacceptability_reason
• usage
• vernacular_languages

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

• 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.