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Integrated Taxonomic Information Service (ITIS) R client
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ritis.Rproj

README.md

ritis

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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}*/")
#> Source: local data frame [10 x 26]
#> 
#>      tsn          nameWInd         nameWOInd             unit1   usage
#>    <chr>             <chr>             <chr>             <chr>   <chr>
#> 1     51     Schizomycetes     Schizomycetes     Schizomycetes invalid
#> 2     50          Bacteria          Bacteria          Bacteria   valid
#> 3     52     Archangiaceae     Archangiaceae     Archangiaceae invalid
#> 4     53   Pseudomonadales   Pseudomonadales   Pseudomonadales   valid
#> 5     54 Rhodobacteriineae Rhodobacteriineae Rhodobacteriineae invalid
#> 6     55  Pseudomonadineae  Pseudomonadineae  Pseudomonadineae invalid
#> 7     56  Nitrobacteraceae  Nitrobacteraceae  Nitrobacteraceae invalid
#> 8     57       Nitrobacter       Nitrobacter       Nitrobacter   valid
#> 9     65      Nitrosomonas      Nitrosomonas      Nitrosomonas   valid
#> 10    70  Thiobacteriaceae  Thiobacteriaceae  Thiobacteriaceae invalid
#> Variables not shown: unacceptReason <chr>, credibilityRating <chr>,
#>   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>, parentTSN
#>   <chr>.

matches only binomials

itis_search(q = "nameWOInd:/[A-Za-z0-9]*[%20]{1,1}[A-Za-z0-9]*/")
#> Source: local data frame [10 x 24]
#> 
#>      tsn                  nameWInd                 nameWOInd        unit1
#>    <chr>                     <chr>                     <chr>        <chr>
#> 1     58        Nitrobacter agilis        Nitrobacter agilis  Nitrobacter
#> 2     59        Nitrobacter flavus        Nitrobacter flavus  Nitrobacter
#> 3     60  Nitrobacter oligotrophis  Nitrobacter oligotrophis  Nitrobacter
#> 4     61   Nitrobacter polytrophus   Nitrobacter polytrophus  Nitrobacter
#> 5     62      Nitrobacter punctata      Nitrobacter punctata  Nitrobacter
#> 6     64  Nitrobacter winogradskyi  Nitrobacter winogradskyi  Nitrobacter
#> 7     66     Nitrosomonas europaea     Nitrosomonas europaea Nitrosomonas
#> 8     67 Nitrosomonas groningensis Nitrosomonas groningensis Nitrosomonas
#> 9     68   Nitrosomonas javenensis   Nitrosomonas javenensis Nitrosomonas
#> 10    69    Nitrosomonas monocella    Nitrosomonas monocella Nitrosomonas
#> Variables not shown: unit2 <chr>, usage <chr>, unacceptReason <chr>,
#>   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>.

REST API

Get accepted names for a TSN

accepted_names(tsn = 504239)
#> Source: local data frame [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)
#> Source: local data frame [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)
#> Source: local data frame [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
#> ..             ...       ...           ...             ...    ...

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.

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