Integrated Taxonomic Information System Client

An interface to the Integrated Taxonomic Information System ('ITIS') (< https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (< https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (< https://www.itis.gov/solr_documentation.html>).


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)

  • 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]*[%20]{0,0}*/")
#> # A tibble: 10 x 27
#>    tsn   nameWInd nameWOInd unit1 usage unacceptReason credibilityRati…
#>    <chr> <chr>    <chr>     <chr> <chr> <chr>          <chr>           
#>  1 51    Schizom… Schizomy… Schi… inva… unavailable, … Minimum taxonom…
#>  2 50    Bacteria Bacteria  Bact… valid <NA>           TWG standards m…
#>  3 52    Archang… Archangi… Arch… inva… unavailable, … Minimum taxonom…
#>  4 53    Pseudom… Pseudomo… Pseu… valid <NA>           TWG standards m…
#>  5 54    Rhodoba… Rhodobac… Rhod… inva… unavailable, … Minimum taxonom…
#>  6 55    Pseudom… Pseudomo… Pseu… inva… unavailable, … Minimum taxonom…
#>  7 56    Nitroba… Nitrobac… Nitr… inva… unavailable, … Minimum taxonom…
#>  8 57    Nitroba… Nitrobac… Nitr… valid <NA>           TWG standards m…
#>  9 65    Nitroso… Nitrosom… Nitr… valid <NA>           TWG standards m…
#> 10 70    Thiobac… Thiobact… Thio… inva… unavailable, … Minimum taxonom…
#> # … with 20 more variables: completenessRating <chr>,
#> #   currencyRating <chr>, kingdom <chr>, rankID <chr>, rank <chr>,
#> #   hierarchySoFar <chr>, hierarchySoFarWRanks <chr>, hierarchyTSN <chr>,
#> #   synonyms <chr>, synonymTSNs <chr>, otherSource <chr>,
#> #   acceptedTSN <chr>, comment <chr>, createDate <chr>, updateDate <chr>,
#> #   `_version_` <dbl>, taxonAuthor <chr>, vernacular <chr>,
#> #   hierarchicalSort <chr>, parentTSN <chr>

matches only binomials

itis_search(q = "nameWOInd:/[A-Za-z0-9]*[%20]{1,1}[A-Za-z0-9]*/")
#> # A tibble: 10 x 25
#>    tsn   nameWInd nameWOInd unit1 unit2 usage unacceptReason
#>    <chr> <chr>    <chr>     <chr> <chr> <chr> <chr>         
#>  1 58    Nitroba… Nitrobac… Nitr… agil… inva… unavailable, …
#>  2 59    Nitroba… Nitrobac… Nitr… flav… inva… unavailable, …
#>  3 60    Nitroba… Nitrobac… Nitr… olig… inva… unavailable, …
#>  4 61    Nitroba… Nitrobac… Nitr… poly… inva… unavailable, …
#>  5 62    Nitroba… Nitrobac… Nitr… punc… inva… unavailable, …
#>  6 64    Nitroba… Nitrobac… Nitr… wino… valid <NA>          
#>  7 66    Nitroso… Nitrosom… Nitr… euro… valid <NA>          
#>  8 67    Nitroso… Nitrosom… Nitr… gron… inva… unavailable, …
#>  9 68    Nitroso… Nitrosom… Nitr… jave… inva… unavailable, …
#> 10 69    Nitroso… Nitrosom… Nitr… mono… inva… unavailable, …
#> # … with 18 more variables: credibilityRating <chr>, kingdom <chr>,
#> #   rankID <chr>, rank <chr>, hierarchySoFar <chr>,
#> #   hierarchySoFarWRanks <chr>, hierarchyTSN <chr>, synonyms <chr>,
#> #   synonymTSNs <chr>, otherSource <chr>, acceptedTSN <chr>,
#> #   comment <chr>, createDate <chr>, updateDate <chr>, `_version_` <dbl>,
#> #   taxonAuthor <chr>, 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.

ropensci_footer

News

ritis 0.7.6

MINOR IMPROVEMENTS

  • improve docs for solr functions, pointing to appropriate docs in solrium package (#12)
  • give link to taxize book in readme, vignette, and pkg level manual file (#13)

BUG FIXES

  • fixed bug in search_anymatch(): we weren't correctly handling cases where no results were returned (#11)

Full diff: https://github.com/ropensci/ritis/compare/v0.7.2...v0.7.6

ritis 0.7.2

NEW FEATURES

  • Integration with vcr and webmockr packages for unit test stubbing

ritis 0.7.0

NEW FEATURES

  • Now using new version of solrium package - users shouldn't see any differences (#9)

ritis 0.6.0

NEW FEATURES

  • Now using crul as underlying HTTP client (#5)

BUG FIXES

  • Base URL change for Solr service from http to https (#8)
  • Fixed JSON parsing problem (#6)

ritis 0.5.4

BUG FIXES

  • Base URL changed from http to https, was causing problems in some requests, but not others. Changed to https (#4)

ritis 0.5.0

NEW FEATURES

  • Re-released to CRAN
  • Complete overhaul of the package API, simplifying all function interfaces, using JSON by default, shorter names, reduce code reuse.
  • Added functions for interacting with ITIS's new Solr interface via use of solrium

ritis 0.0.3

BUG FIXES

  • Removed dependency on plyr - moved from laply to lapply across functions.

ritis 0.0.2

BUG FIXES

  • Temporarily removed all tests until they can be fixed and updated, and so that package passes checks.

ritis 0.0.1

NEW FEATURES

  • released to CRAN

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("ritis")

0.7.6 by Scott Chamberlain, 6 months ago


https://github.com/ropensci/ritis


Report a bug at https://github.com/ropensci/ritis/issues


Browse source code at https://github.com/cran/ritis


Authors: Scott Chamberlain [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports solrium, crul, jsonlite, data.table, tibble

Suggests roxygen2, knitr, testthat, webmockr, vcr


Imported by camtrapR, taxize.


See at CRAN