Introduction to the wikitaxa package

The goal of wikitaxa is to allow search and taxonomic data retrieval from across many Wikimedia sites, including: Wikipedia, Wikicommons, and Wikispecies.

Low level API

The low level API is meant for power users and gives you more control, but requires more knowledge.

wt_wiki_page()
wt_wiki_page_parse()
wt_wiki_url_build()
wt_wiki_url_parse()
wt_wikispecies_parse()
wt_wikicommons_parse()
wt_wikipedia_parse()

High level API

The high level API is meant to be easier and faster to use.

wt_data()
wt_data_id()
wt_wikispecies()
wt_wikicommons()
wt_wikipedia()

Search functions:

wt_wikicommons_search()
wt_wikispecies_search()
wt_wikipedia_search()

Installation

CRAN version

install.packages("wikitaxa")

Dev version

devtools::install_github("ropensci/wikitaxa")

library("wikitaxa")

wiki data

wt_data("Poa annua")

Get a Wikidata ID

wt_data_id("Mimulus foliatus")
#> [1] "Q6495130"
#> attr(,"class")
#> [1] "wiki_id"

wikipedia

lower level

pg <- wt_wiki_page("https://en.wikipedia.org/wiki/Malus_domestica")
res <- wt_wiki_page_parse(pg)
res$iwlinks
#> [1] "https://en.wiktionary.org/wiki/apple"                                  
#> [2] "https://commons.wikimedia.org/wiki/Special:Search/Apple"               
#> [3] "https://en.wikiquote.org/wiki/Apples"                                  
#> [4] "https://en.wikisource.org/wiki/1911_Encyclop%C3%A6dia_Britannica/Apple"
#> [5] "https://en.wikibooks.org/wiki/Apples"                                  
#> [6] "https://species.wikimedia.org/wiki/Malus_domestica"                    
#> [7] "https://commons.wikimedia.org/wiki/Category:Apple_cultivars"

higher level

res <- wt_wikipedia("Malus domestica")
res$common_names
#> # A tibble: 3 × 2
#>         name language
#>        <chr>    <chr>
#> 1 apple tree       en
#> 2      apple       en
#> 3      Apple       en
res$classification
#> # A tibble: 9 × 2
#>       rank         name
#>      <chr>        <chr>
#> 1  kingdom      Plantae
#> 2 unranked  Angiosperms
#> 3 unranked     Eudicots
#> 4 unranked       Rosids
#> 5    order      Rosales
#> 6   family     Rosaceae
#> 7    genus        Malus
#> 8  species    M. pumila
#> 9 binomial Malus pumila

choose a wikipedia language

# French
wt_wikipedia(name = "Malus domestica", wiki = "fr")
# Slovak
wt_wikipedia(name = "Malus domestica", wiki = "sk")
# Vietnamese
wt_wikipedia(name = "Malus domestica", wiki = "vi")

wt_wikipedia_search(query = "Pinus")
#> $batchcomplete
#> [1] ""
#> 
#> $continue
#> $continue$sroffset
#> [1] 10
#> 
#> $continue$continue
#> [1] "-||"
#> 
#> 
#> $query
#> $query$searchinfo
#> $query$searchinfo$totalhits
#> [1] 2804
#> 
#> 
#> $query$search
#> # A tibble: 10 × 6
#>       ns                 title  size wordcount
#> *  <int>                 <chr> <int>     <int>
#> 1      0                  Pine 19915      2372
#> 2      0 List of Pinus species 13999       995
#> 3      0      Pinus luchuensis  2903       166
#> 4      0     Pinus wallichiana  4295       433
#> 5      0           Pinus nigra 11468      1352
#> 6      0          Pinus kesiya  5281       512
#> 7      0       Pinus devoniana  3801       397
#> 8      0  Pinus × sondereggeri  3485       347
#> 9      0            Pinus mugo 10884       795
#> 10     0     Pinus heldreichii  6482       707
#> # ... with 2 more variables: snippet <chr>, timestamp <chr>

search supports languages

wt_wikipedia_search(query = "Pinus", wiki = "fr")

wikicommons

lower level

pg <- wt_wiki_page("https://commons.wikimedia.org/wiki/Abelmoschus")
res <- wt_wikicommons_parse(pg)
res$common_names[1:3]
#> [[1]]
#> [[1]]$name
#> [1] "okra"
#> 
#> [[1]]$language
#> [1] "en"
#> 
#> 
#> [[2]]
#> [[2]]$name
#> [1] "مسكي"
#> 
#> [[2]]$language
#> [1] "ar"
#> 
#> 
#> [[3]]
#> [[3]]$name
#> [1] "Abelmoş"
#> 
#> [[3]]$language
#> [1] "az"

higher level

res <- wt_wikicommons("Abelmoschus")
res$classification
#> # A tibble: 15 × 2
#>            rank           name
#>           <chr>          <chr>
#> 1        Domain      Eukaryota
#> 2    • unranked Archaeplastida
#> 3      • Regnum        Plantae
#> 4      • Cladus    angiosperms
#> 5      • Cladus       eudicots
#> 6      • Cladus  core eudicots
#> 7      • Cladus    superrosids
#> 8      • Cladus         rosids
#> 9      • Cladus    eurosids II
#> 10       • Ordo       Malvales
#> 11    • Familia      Malvaceae
#> 12 • Subfamilia     Malvoideae
#> 13     • Tribus      Hibisceae
#> 14            •    Abelmoschus
#> 15               Medik. (1787)
res$common_names
#> # A tibble: 18 × 2
#>             name language
#>            <chr>    <chr>
#> 1           okra       en
#> 2           مسكي       ar
#> 3        Abelmoş       az
#> 4      Ibiškovec       cs
#> 5   Bisameibisch       de
#> 6          Okrat       fi
#> 7      Abelmosco       gl
#> 8      Abelmošus       hr
#> 9         Ybiškė       lt
#> 10  അബെ\u0d7dമോസ്കസ്       ml
#> 11      Абельмош      mrj
#> 12       Piżmian       pl
#> 13      Абельмош       ru
#> 14          موري       sd
#> 15   Okrasläktet       sv
#> 16      Абельмош      udm
#> 17 Chi Vông vang       vi
#> 18        黄葵属       zh

wt_wikicommons_search(query = "Pinus")
#> $batchcomplete
#> [1] ""
#> 
#> $continue
#> $continue$sroffset
#> [1] 10
#> 
#> $continue$continue
#> [1] "-||"
#> 
#> 
#> $query
#> $query$searchinfo
#> $query$searchinfo$totalhits
#> [1] 257
#> 
#> 
#> $query$search
#> # A tibble: 10 × 6
#>       ns                                    title  size wordcount
#> *  <int>                                    <chr> <int>     <int>
#> 1      0                                    Pinus  4160       303
#> 2      0                              Pinus nigra  7449       486
#> 3      0                       Pinus × schwerinii   634        67
#> 4      0                               Pinus mugo  7157       573
#> 5      0                             Spinus pinus  1563       242
#> 6      0                       Pinus tabuliformis  1739       136
#> 7      0                          Setophaga pinus  1735       198
#> 8      0                          Pinus sabiniana  2799       217
#> 9      0 Pinus distribution maps of North America 25971        92
#> 10     0                            Pinus cooperi   564        64
#> # ... with 2 more variables: snippet <chr>, timestamp <chr>

wikispecies

lower level

pg <- wt_wiki_page("https://species.wikimedia.org/wiki/Malus_domestica")
res <- wt_wikispecies_parse(pg, types = "common_names")
res$common_names[1:3]
#> [[1]]
#> [[1]]$name
#> [1] "Ябълка"
#> 
#> [[1]]$language
#> [1] "български"
#> 
#> 
#> [[2]]
#> [[2]]$name
#> [1] "Poma, pomera"
#> 
#> [[2]]$language
#> [1] "català"
#> 
#> 
#> [[3]]
#> [[3]]$name
#> [1] "Apfel"
#> 
#> [[3]]$language
#> [1] "Deutsch"

higher level

res <- wt_wikispecies("Malus domestica")
res$classification
#> # A tibble: 8 × 2
#>          rank          name
#>         <chr>         <chr>
#> 1 Superregnum     Eukaryota
#> 2      Regnum       Plantae
#> 3      Cladus   Angiosperms
#> 4      Cladus      Eudicots
#> 5      Cladus Core eudicots
#> 6      Cladus        Rosids
#> 7      Cladus    Eurosids I
#> 8        Ordo       Rosales
res$common_names
#> # A tibble: 19 × 2
#>               name   language
#>              <chr>      <chr>
#> 1           Ябълка  български
#> 2     Poma, pomera     català
#> 3            Apfel    Deutsch
#> 4      Aed-õunapuu      eesti
#> 5            Μηλιά   Ελληνικά
#> 6            Apple    English
#> 7          Manzano    español
#> 8            Pomme   français
#> 9            Melâr     furlan
#> 10        사과나무     한국어
#> 11          ‘Āpala    Hawaiʻi
#> 12            Melo   italiano
#> 13           Aapel Nordfriisk
#> 14  Maçã, Macieira  português
#> 15 Яблоня домашняя    русский
#> 16   Tarhaomenapuu      suomi
#> 17            Elma     Türkçe
#> 18  Яблуня домашня українська
#> 19          Pomaro     vèneto

wt_wikispecies_search(query = "Pinus")
#> $batchcomplete
#> [1] ""
#> 
#> $continue
#> $continue$sroffset
#> [1] 10
#> 
#> $continue$continue
#> [1] "-||"
#> 
#> 
#> $query
#> $query$searchinfo
#> $query$searchinfo$totalhits
#> [1] 396
#> 
#> 
#> $query$search
#> # A tibble: 10 × 6
#>       ns                    title  size wordcount
#> *  <int>                    <chr> <int>     <int>
#> 1      0                    Pinus  1570       282
#> 2      0        Pinus subg. Pinus   318        27
#> 3      0             Pinus clausa  1183       211
#> 4      0        Pinus sect. Pinus   623        68
#> 5      0           Pinus resinosa  1195       166
#> 6      0 Pinus nigra subsp. nigra  1412       127
#> 7      0            Pinus cooperi   680        89
#> 8      0         Pinus thunbergii   873       122
#> 9      0         Pinus gordoniana   594        61
#> 10     0     Pinus subsect. Pinus   718        94
#> # ... with 2 more variables: snippet <chr>, timestamp <chr>

Introduction to the wikitaxa package

Scott Chamberlain

2017-05-05

Low level API

High level API

Installation

wiki data

wikipedia

wikicommons

wikispecies