ritis vignette


for v0.6.0


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

Installation

install.packages("ritis")

Or development version from GitHub

install.packages("devtools")
devtools::install_github("ropensci/ritis")

Usage

library("ritis")

ITIS Solr interface

There are four methods.

  • itis_search() - Search
  • itis_group() - Group
  • itis_highlight() - Hightlight
  • itis_facet() - Facet

These four methods use the equivalent functions in the package solrium, e.g., ritis::itis_search() uses solrium::solr_search(), etc. The itis_*() functions simply use ... to allow users to pass on parameters to the wrapped solrium functions. So do read the solrium docs.

ITIS Solr API docs: http://www.itis.gov/solr_documentation.html

Some examples:

matches only monomials

itis_search(q = "nameWOInd:/[A-Za-z0-9]*[%20]{0,0}*/")

#> # A tibble: 10 x 27
#>      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
#> # ... with 22 more variables: 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>,
#> #   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
#>    <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
#> # ... with 21 more variables: 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>, hierarchicalSort <chr>

ITIS REST API interface

ITIS REST API docs: http://www.itis.gov/ws_description.html

The following are some example uses. There are many more methods not shown below

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

Citing

Scott Chamberlain (2017). ritis: Integrated Taxonomic Information System Client. R package version 0.6.0. https://CRAN.R-project.org/package=ritis

License and bugs

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