wikitaxa - Taxonomy data from Wikipedia
The goal of wikitaxa is to allow search and taxonomic data retrieval from across many Wikimedia sites, including: Wikipedia, Wikicommons, and Wikispecies.
There are lower level and higher level parts to the package 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()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()CRAN version
install.packages("wikitaxa")Dev version
remotes::install_github("ropensci/wikitaxa")library("wikitaxa")z <- wt_data("Poa annua")
names(z)
#> [1] "labels" "descriptions" "aliases" "sitelinks" "claims"
head(z$labels)
#> language value
#> 1 pt Poa annua
#> 2 is Varpasveifgras
#> 3 pl Wiechlina roczna
#> 4 fr Pâturin annuel
#> 5 es Poa annua
#> 6 en Poa annuaGet a Wikidata ID
wt_data_id("Mimulus foliatus")
#> [1] "Q6495130"
#> attr(,"class")
#> [1] "wiki_id"lower level
pg <- wt_wiki_page("https://en.wikipedia.org/wiki/Malus_domestica")
res <- wt_wiki_page_parse(pg)
res$iwlinks
#> [1] "https://commons.wikimedia.org/wiki/Category:Apples"
#> [2] "https://commons.wikimedia.org/wiki/Category:Apple_cultivars"
#> [3] "https://www.wikidata.org/wiki/Q158657"
#> [4] "https://www.wikidata.org/wiki/Q18674606"
#> [5] "https://species.wikimedia.org/wiki/Malus_pumila"
#> [6] "https://species.wikimedia.org/wiki/Malus_domestica"higher level
res <- wt_wikipedia("Malus domestica")
res$common_names
#> # A tibble: 1 x 2
#> name language
#> <chr> <chr>
#> 1 Apple en
res$classification
#> # A tibble: 3 x 2
#> rank name
#> <chr> <chr>
#> 1 plainlinks ""
#> 2 binomial "Malus domestica"
#> 3 <NA> ""choose a wikipedia language
# French
wt_wikipedia(name = "Malus domestica", wiki = "fr")
#> $langlinks
#> # A tibble: 60 x 5
#> lang url langname autonym `*`
#> <chr> <chr> <chr> <chr> <chr>
#> 1 als https://als.wikipedia.org/wiki/Kultu… Alemannis… Alemannis… Kulturapf…
#> 2 am https://am.wikipedia.org/wiki/%E1%89… amharique አማርኛ ቱፋሕ
#> 3 ast https://ast.wikipedia.org/wiki/Malus… asturien asturianu Malus dom…
#> 4 az https://az.wikipedia.org/wiki/M%C9%9… azéri azərbayca… Mədəni al…
#> 5 bat-s… https://bat-smg.wikipedia.org/wiki/V… Samogitian žemaitėška Vuobelės
#> 6 bg https://bg.wikipedia.org/wiki/%D0%94… bulgare български Домашна я…
#> 7 bpy https://bpy.wikipedia.org/wiki/%E0%A… bishnupri… বিষ্ণুপ্র… আপেল
#> 8 ca https://ca.wikipedia.org/wiki/Pomera… catalan català Pomera co…
#> 9 cs https://cs.wikipedia.org/wiki/Jablo%… tchèque čeština Jabloň do…
#> 10 csb https://csb.wikipedia.org/wiki/Dom%C… kachoube kaszëbsczi Domôcô ja…
#> # … with 50 more rows
#>
#> $externallinks
#> [1] "http://www.cabi-publishing.org/pdf/Books/0851995926/0851995926_Chap01.pdf"
#> [2] "http://www.umass.edu/fruitadvisor/fruitnotes/ontheorigin.pdf"
#> [3] "http://www.applegenome.org"
#> [4] "http://societeradio-canada.info/emissions/les_annees_lumiere/2010-2011/"
#> [5] "http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.654.html"
#> [6] "https://gallica.bnf.fr/ark:/12148/bpt6k28582v"
#> [7] "http://worldcat.org/issn/1471-2229&lang=fr"
#> [8] "https://www.ncbi.nlm.nih.gov/pubmed/26924309"
#> [9] "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4770685"
#> [10] "https://dx.doi.org/10.1186%2Fs12870-016-0739-y"
#> [11] "https://doi.org/10.1186/s12870-016-0739-y"
#> [12] "http://www.hamblenne.be/LISTE_RGF.pdf"
#> [13] "http://www.arcticapples.com/blog/john/demystifying-arctic-apples#.UaeX-Jzjmw5"
#> [14] "http://www.cctec.cornell.edu/plants/GENEVA-Apple-Rootstocks-Comparison-Chart-120911.pdf"
#> [15] "https://commons.wikimedia.org/wiki/Category:Malus_domestica?uselang=fr"
#> [16] "http://www.tela-botanica.org/page:eflore"
#> [17] "http://www.tela-botanica.org/bdtfx-nn-40744"
#> [18] "http://www.cbif.gc.ca/acp/fra/siti/regarder?tsn=516655"
#> [19] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=516655"
#> [20] "http://www.cbif.gc.ca/acp/fra/siti/regarder?tsn=25262"
#> [21] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=25262"
#> [22] "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lin=s&p=has_linkout&id=3750"
#> [23] "http://www.ars-grin.gov/"
#> [24] "https://npgsweb.ars-grin.gov/gringlobal/taxonomydetail.aspx?104681"
#> [25] "https://www.biolib.cz/en/"
#> [26] "https://www.biolib.cz/en/taxon/id39552/"
#> [27] "http://inpn.mnhn.fr/isb/espece/cd_nom/107207"
#> [28] "http://www.bmlisieux.com/normandie/roblet.htm"
#> [29] "http://site.voila.fr/babadubonsai/docum/docmal.html"
#> [30] "http://www.fruitiers.net"
#> [31] "http://www.inra.fr/hyppz/CULTURES/3c---003.htm"
#> [32] "http://cat.inist.fr/?aModele=afficheN&cpsidt=15506238"
#> [33] "http://www.omafra.gov.on.ca/french/crops/facts/98-014.htm"
#> [34] "http://www.gardenaction.co.uk/fruit_veg_diary/fruit_veg_mini_project_september_2_apple.asp"
#>
#> $common_names
#> # A tibble: 1 x 2
#> name language
#> <chr> <chr>
#> 1 Pommier domestique fr
#>
#> $classification
#> # A tibble: 0 x 0
#>
#> $synonyms
#> list()
# Slovak
wt_wikipedia(name = "Malus domestica", wiki = "sk")
#> $langlinks
#> # A tibble: 60 x 5
#> lang url langname autonym `*`
#> <chr> <chr> <chr> <chr> <chr>
#> 1 als https://als.wikipedia.org/wiki/K… Alemannisch Alemannis… Kulturap…
#> 2 am https://am.wikipedia.org/wiki/%E… amharčina አማርኛ ቱፋሕ
#> 3 ast https://ast.wikipedia.org/wiki/M… astúrčina asturianu Malus do…
#> 4 az https://az.wikipedia.org/wiki/M%… azerbajdžančina azərbayca… Mədəni a…
#> 5 bat-s… https://bat-smg.wikipedia.org/wi… Samogitian žemaitėška Vuobelės
#> 6 bg https://bg.wikipedia.org/wiki/%D… bulharčina български Домашна …
#> 7 bpy https://bpy.wikipedia.org/wiki/%… bišnuprijskoma… বিষ্ণুপ্র… আপেল
#> 8 ca https://ca.wikipedia.org/wiki/Po… katalánčina català Pomera c…
#> 9 cs https://cs.wikipedia.org/wiki/Ja… čeština čeština Jabloň d…
#> 10 csb https://csb.wikipedia.org/wiki/D… kašubčina kaszëbsczi Domôcô j…
#> # … with 50 more rows
#>
#> $externallinks
#> list()
#>
#> $common_names
#> # A tibble: 1 x 2
#> name language
#> <chr> <chr>
#> 1 Jabloň domáca sk
#>
#> $classification
#> # A tibble: 0 x 0
#>
#> $synonyms
#> list()
# Vietnamese
wt_wikipedia(name = "Malus domestica", wiki = "vi")
#> $langlinks
#> # A tibble: 60 x 5
#> lang url langname autonym `*`
#> <chr> <chr> <chr> <chr> <chr>
#> 1 als https://als.wikipedia.org/wiki/Kul… Alemannisch Alemanni… Kulturapf…
#> 2 am https://am.wikipedia.org/wiki/%E1%… Tiếng Amha… አማርኛ ቱፋሕ
#> 3 ast https://ast.wikipedia.org/wiki/Mal… Tiếng Astu… asturianu Malus dom…
#> 4 az https://az.wikipedia.org/wiki/M%C9… Tiếng Azer… azərbayc… Mədəni al…
#> 5 zh-min-… https://zh-min-nan.wikipedia.org/w… Chinese (M… Bân-lâm-… Phōng-kó-…
#> 6 bg https://bg.wikipedia.org/wiki/%D0%… Tiếng Bulg… български Домашна я…
#> 7 ca https://ca.wikipedia.org/wiki/Pome… Tiếng Cata… català Pomera co…
#> 8 cs https://cs.wikipedia.org/wiki/Jabl… Tiếng Séc čeština Jabloň do…
#> 9 da https://da.wikipedia.org/wiki/Almi… Tiếng Đan … dansk Almindeli…
#> 10 de https://de.wikipedia.org/wiki/Kult… Tiếng Đức Deutsch Kulturapf…
#> # … w