Package 'wikitaxa' reference manual

Title:	Taxonomic Information from 'Wikipedia'
Description:	'Taxonomic' information from 'Wikipedia', 'Wikicommons', 'Wikispecies', and 'Wikidata'. Functions included for getting taxonomic information from each of the sources just listed, as well performing taxonomic search.
Authors:	Scott Chamberlain [aut], Ethan Welty [aut], Grzegorz Sapijaszko [aut], Zachary Foster [aut, cre]
Maintainer:	Zachary Foster <[email protected]>
License:	MIT + file LICENSE
Version:	0.4.0.91
Built:	2024-10-11 20:16:49 UTC
Source:	https://github.com/ropensci/wikitaxa

wikitaxa

Description

Taxonomic Information from Wikipedia

Author(s)

Scott Chamberlain [email protected]

Ethan Welty

List of Wikipedias

Description

data.frame of 295 rows, with 3 columns:

language - language
language_local - language in local name
wiki - langugae code for the wiki

Details

From https://meta.wikimedia.org/wiki/List_of_Wikipedias

Wikidata taxonomy data

Description

Wikidata taxonomy data

Usage

wt_data(x, property = NULL, ...)

wt_data_id(x, language = "en", limit = 10, ...)
wt_data(x, property = NULL, ...)

wt_data_id(x, language = "en", limit = 10, ...)

Arguments

`x`	(character) a taxonomic name
`property`	(character) a property id, e.g., P486
`...`	curl options passed on to `httr::GET()`
`language`	(character) two letter language code
`limit`	(integer) records to return. Default: 10

Details

Note that wt_data can take a while to run since when fetching claims it has to do so one at a time for each claim

You can search things other than taxonomic names with wt_data if you like

Value

wt_data searches Wikidata, and returns a list with elements:

labels - data.frame with columns: language, value
descriptions - data.frame with columns: language, value
aliases - data.frame with columns: language, value
sitelinks - data.frame with columns: site, title
claims - data.frame with columns: claims, property_value, property_description, value (comma separted values in string)

wt_data_id gets the Wikidata ID for the searched term, and returns the ID as character

Examples

## Not run: 
# search by taxon name
# wt_data("Mimulus alsinoides")

# choose which properties to return
wt_data(x="Mimulus foliatus", property = c("P846", "P815"))

# get a taxonomic identifier
wt_data_id("Mimulus foliatus")
# the id can be passed directly to wt_data()
# wt_data(wt_data_id("Mimulus foliatus"))

## End(Not run)
## Not run: 
# search by taxon name
# wt_data("Mimulus alsinoides")

# choose which properties to return
wt_data(x="Mimulus foliatus", property = c("P846", "P815"))

# get a taxonomic identifier
wt_data_id("Mimulus foliatus")
# the id can be passed directly to wt_data()
# wt_data(wt_data_id("Mimulus foliatus"))

## End(Not run)

Get MediaWiki Page from API

Description

Supports both static page urls and their equivalent API calls.

Usage

wt_wiki_page(url, ...)
wt_wiki_page(url, ...)

Arguments

`url`	(character) MediaWiki page url.
`...`	Arguments passed to `wt_wiki_url_build()` if `url` is a static page url.

Details

If the URL given is for a human readable html page, we convert it to equivalent API call - if URL is already an API call, we just use that.

Value

an HttpResponse response object from crul

Examples

## Not run: 
wt_wiki_page("https://en.wikipedia.org/wiki/Malus_domestica")

## End(Not run)
## Not run: 
wt_wiki_page("https://en.wikipedia.org/wiki/Malus_domestica")

## End(Not run)

Parse MediaWiki Page

Description

Parses common properties from the result of a MediaWiki API page call.

Usage

wt_wiki_page_parse(
  page,
  types = c("langlinks", "iwlinks", "externallinks"),
  tidy = FALSE
)
wt_wiki_page_parse(
  page,
  types = c("langlinks", "iwlinks", "externallinks"),
  tidy = FALSE
)

Arguments

`page`	(crul::HttpResponse) Result of `wt_wiki_page()`
`types`	(character) List of properties to parse.
`tidy`	(logical). tidy output to data.frames when possible. Default: `FALSE`

Details

Available properties currently not parsed: title, displaytitle, pageid, revid, redirects, text, categories, links, templates, images, sections, properties, ...

Value

a list

Examples

## Not run: 
pg <- wt_wiki_page("https://en.wikipedia.org/wiki/Malus_domestica")
wt_wiki_page_parse(pg)

## End(Not run)
## Not run: 
pg <- wt_wiki_page("https://en.wikipedia.org/wiki/Malus_domestica")
wt_wiki_page_parse(pg)

## End(Not run)

Build MediaWiki Page URL

Description

Builds a MediaWiki page url from its component parts (wiki name, wiki type, and page title). Supports both static page urls and their equivalent API calls.

Usage

wt_wiki_url_build(
  wiki,
  type = NULL,
  page = NULL,
  api = FALSE,
  action = "parse",
  redirects = TRUE,
  format = "json",
  utf8 = TRUE,
  prop = c("text", "langlinks", "categories", "links", "templates", "images",
    "externallinks", "sections", "revid", "displaytitle", "iwlinks", "properties")
)
wt_wiki_url_build(
  wiki,
  type = NULL,
  page = NULL,
  api = FALSE,
  action = "parse",
  redirects = TRUE,
  format = "json",
  utf8 = TRUE,
  prop = c("text", "langlinks", "categories", "links", "templates", "images",
    "externallinks", "sections", "revid", "displaytitle", "iwlinks", "properties")
)

Arguments

`wiki`	(character \| list) Either the wiki name or a list with `⁠$wiki⁠`, `⁠$type⁠`, and `⁠$page⁠` (the output of `wt_wiki_url_parse()`).
`type`	(character) Wiki type.
`page`	(character) Wiki page title.
`api`	(boolean) Whether to return an API call or a static page url (default). If `FALSE`, all following (API-only) arguments are ignored.
`action`	(character) See https://en.wikipedia.org/w/api.php for supported actions. This function currently only supports "parse".
`redirects`	(boolean) If the requested page is set to a redirect, resolve it.
`format`	(character) See https://en.wikipedia.org/w/api.php for supported output formats.
`utf8`	(boolean) If `TRUE`, encodes most (but not all) non-ASCII characters as UTF-8 instead of replacing them with hexadecimal escape sequences.
`prop`	(character) Properties to retrieve, either as a character vector or pipe-delimited string. See https://en.wikipedia.org/w/api.php?action=help&modules=parse for supported properties.

Value

a URL (character)

Examples

wt_wiki_url_build(wiki = "en", type = "wikipedia", page = "Malus domestica")
wt_wiki_url_build(
  wt_wiki_url_parse("https://en.wikipedia.org/wiki/Malus_domestica"))
wt_wiki_url_build("en", "wikipedia", "Malus domestica", api = TRUE)
wt_wiki_url_build(wiki = "en", type = "wikipedia", page = "Malus domestica")
wt_wiki_url_build(
  wt_wiki_url_parse("https://en.wikipedia.org/wiki/Malus_domestica"))
wt_wiki_url_build("en", "wikipedia", "Malus domestica", api = TRUE)

Parse MediaWiki Page URL

Description

Parse a MediaWiki page url into its component parts (wiki name, wiki type, and page title). Supports both static page urls and their equivalent API calls.

Usage

wt_wiki_url_parse(url)
wt_wiki_url_parse(url)

Arguments

url

(character) MediaWiki page url.

Value

a list with elements:

wiki - wiki language
type - wikipedia type
page - page name

Examples

wt_wiki_url_parse(url="https://en.wikipedia.org/wiki/Malus_domestica")
wt_wiki_url_parse("https://en.wikipedia.org/w/api.php?page=Malus_domestica")
wt_wiki_url_parse(url="https://en.wikipedia.org/wiki/Malus_domestica")
wt_wiki_url_parse("https://en.wikipedia.org/w/api.php?page=Malus_domestica")

WikiCommons

Description

WikiCommons

Usage

wt_wikicommons(name, utf8 = TRUE, ...)

wt_wikicommons_parse(
  page,
  types = c("langlinks", "iwlinks", "externallinks", "common_names", "classification"),
  tidy = FALSE
)

wt_wikicommons_search(query, limit = 10, offset = 0, utf8 = TRUE, ...)
wt_wikicommons(name, utf8 = TRUE, ...)

wt_wikicommons_parse(
  page,
  types = c("langlinks", "iwlinks", "externallinks", "common_names", "classification"),
  tidy = FALSE
)

wt_wikicommons_search(query, limit = 10, offset = 0, utf8 = TRUE, ...)

Arguments

`name`	(character) Wiki name - as a page title, must be length 1
`utf8`	(logical) If `TRUE`, encodes most (but not all) non-ASCII characters as UTF-8 instead of replacing them with hexadecimal escape sequences. Default: `TRUE`
`...`	curl options, passed on to `httr::GET()`
`page`	(`httr::response()`) Result of `wt_wiki_page()`
`types`	(character) List of properties to parse
`tidy`	(logical). tidy output to data.frame's if possible. Default: `FALSE`
`query`	(character) query terms
`limit`	(integer) number of results to return. Default: 10
`offset`	(integer) record to start at. Default: 0

Value

wt_wikicommons returns a list, with slots:

langlinks - language page links
externallinks - external links
common_names - a data.frame with name and language columns
classification - a data.frame with rank and name columns

wt_wikicommons_parse returns a list

wt_wikicommons_search returns a list with slots for continue and query, where query holds the results, with query$search slot with the search results

References

https://www.mediawiki.org/wiki/API:Search for help on search

Examples

## Not run: 
# high level
wt_wikicommons(name = "Malus domestica")
wt_wikicommons(name = "Pinus contorta")
wt_wikicommons(name = "Ursus americanus")
wt_wikicommons(name = "Balaenoptera musculus")

wt_wikicommons(name = "Category:Poeae")
wt_wikicommons(name = "Category:Pinaceae")

# low level
pg <- wt_wiki_page("https://commons.wikimedia.org/wiki/Malus_domestica")
wt_wikicommons_parse(pg)

# search wikicommons
# FIXME: utf=FALSE for now until curl::curl_escape fix 
# https://github.com/jeroen/curl/issues/228
wt_wikicommons_search(query = "Pinus", utf8 = FALSE)

## use search results to dig into pages
res <- wt_wikicommons_search(query = "Pinus", utf8 = FALSE)
lapply(res$query$search$title[1:3], wt_wikicommons)

## End(Not run)
## Not run: 
# high level
wt_wikicommons(name = "Malus domestica")
wt_wikicommons(name = "Pinus contorta")
wt_wikicommons(name = "Ursus americanus")
wt_wikicommons(name = "Balaenoptera musculus")

wt_wikicommons(name = "Category:Poeae")
wt_wikicommons(name = "Category:Pinaceae")

# low level
pg <- wt_wiki_page("https://commons.wikimedia.org/wiki/Malus_domestica")
wt_wikicommons_parse(pg)

# search wikicommons
# FIXME: utf=FALSE for now until curl::curl_escape fix 
# https://github.com/jeroen/curl/issues/228
wt_wikicommons_search(query = "Pinus", utf8 = FALSE)

## use search results to dig into pages
res <- wt_wikicommons_search(query = "Pinus", utf8 = FALSE)
lapply(res$query$search$title[1:3], wt_wikicommons)

## End(Not run)

Wikipedia

Description

Wikipedia

Usage

wt_wikipedia(name, wiki = "en", utf8 = TRUE, ...)

wt_wikipedia_parse(
  page,
  types = c("langlinks", "iwlinks", "externallinks", "common_names", "classification"),
  tidy = FALSE
)

wt_wikipedia_search(
  query,
  wiki = "en",
  limit = 10,
  offset = 0,
  utf8 = TRUE,
  ...
)
wt_wikipedia(name, wiki = "en", utf8 = TRUE, ...)

wt_wikipedia_parse(
  page,
  types = c("langlinks", "iwlinks", "externallinks", "common_names", "classification"),
  tidy = FALSE
)

wt_wikipedia_search(
  query,
  wiki = "en",
  limit = 10,
  offset = 0,
  utf8 = TRUE,
  ...
)

Arguments

`name`	(character) Wiki name - as a page title, must be length 1
`wiki`	(character) wiki language. default: en. See wikipedias for language codes.
`utf8`	(logical) If `TRUE`, encodes most (but not all) non-ASCII characters as UTF-8 instead of replacing them with hexadecimal escape sequences. Default: `TRUE`
`...`	curl options, passed on to `httr::GET()`
`page`	(`httr::response()`) Result of `wt_wiki_page()`
`types`	(character) List of properties to parse
`tidy`	(logical). tidy output to data.frame's if possible. Default: `FALSE`
`query`	(character) query terms
`limit`	(integer) number of results to return. Default: 10
`offset`	(integer) record to start at. Default: 0

Value

wt_wikipedia returns a list, with slots:

langlinks - language page links
externallinks - external links
common_names - a data.frame with name and language columns
classification - a data.frame with rank and name columns
synonyms - a character vector with taxonomic names

wt_wikipedia_parse returns a list with same slots determined by the types parmeter

wt_wikipedia_search returns a list with slots for continue and query, where query holds the results, with query$search slot with the search results

References

https://www.mediawiki.org/wiki/API:Search for help on search

Examples

## Not run: 
# high level
wt_wikipedia(name = "Malus domestica")
wt_wikipedia(name = "Malus domestica", wiki = "fr")
wt_wikipedia(name = "Malus domestica", wiki = "da")

# low level
pg <- wt_wiki_page("https://en.wikipedia.org/wiki/Malus_domestica")
wt_wikipedia_parse(pg)
wt_wikipedia_parse(pg, tidy = TRUE)

# search wikipedia
# FIXME: utf=FALSE for now until curl::curl_escape fix 
# https://github.com/jeroen/curl/issues/228
wt_wikipedia_search(query = "Pinus", utf8=FALSE)
wt_wikipedia_search(query = "Pinus", wiki = "fr", utf8=FALSE)
wt_wikipedia_search(query = "Pinus", wiki = "br", utf8=FALSE)

## curl options
# wt_wikipedia_search(query = "Pinus", verbose = TRUE, utf8=FALSE)

## use search results to dig into pages
res <- wt_wikipedia_search(query = "Pinus", utf8=FALSE)
lapply(res$query$search$title[1:3], wt_wikipedia)

## End(Not run)
## Not run: 
# high level
wt_wikipedia(name = "Malus domestica")
wt_wikipedia(name = "Malus domestica", wiki = "fr")
wt_wikipedia(name = "Malus domestica", wiki = "da")

# low level
pg <- wt_wiki_page("https://en.wikipedia.org/wiki/Malus_domestica")
wt_wikipedia_parse(pg)
wt_wikipedia_parse(pg, tidy = TRUE)

# search wikipedia
# FIXME: utf=FALSE for now until curl::curl_escape fix 
# https://github.com/jeroen/curl/issues/228
wt_wikipedia_search(query = "Pinus", utf8=FALSE)
wt_wikipedia_search(query = "Pinus", wiki = "fr", utf8=FALSE)
wt_wikipedia_search(query = "Pinus", wiki = "br", utf8=FALSE)

## curl options
# wt_wikipedia_search(query = "Pinus", verbose = TRUE, utf8=FALSE)

## use search results to dig into pages
res <- wt_wikipedia_search(query = "Pinus", utf8=FALSE)
lapply(res$query$search$title[1:3], wt_wikipedia)

## End(Not run)

WikiSpecies

Description

WikiSpecies

Usage

wt_wikispecies(name, utf8 = TRUE, ...)

wt_wikispecies_parse(
  page,
  types = c("langlinks", "iwlinks", "externallinks", "common_names", "classification"),
  tidy = FALSE
)

wt_wikispecies_search(query, limit = 10, offset = 0, utf8 = TRUE, ...)
wt_wikispecies(name, utf8 = TRUE, ...)

wt_wikispecies_parse(
  page,
  types = c("langlinks", "iwlinks", "externallinks", "common_names", "classification"),
  tidy = FALSE
)

wt_wikispecies_search(query, limit = 10, offset = 0, utf8 = TRUE, ...)

Arguments

`name`	(character) Wiki name - as a page title, must be length 1
`utf8`	(logical) If `TRUE`, encodes most (but not all) non-ASCII characters as UTF-8 instead of replacing them with hexadecimal escape sequences. Default: `TRUE`
`...`	curl options, passed on to `httr::GET()`
`page`	(`httr::response()`) Result of `wt_wiki_page()`
`types`	(character) List of properties to parse
`tidy`	(logical). tidy output to data.frame's if possible. Default: `FALSE`
`query`	(character) query terms
`limit`	(integer) number of results to return. Default: 10
`offset`	(integer) record to start at. Default: 0

Value

wt_wikispecies returns a list, with slots:

langlinks - language page links
externallinks - external links
common_names - a data.frame with name and language columns
classification - a data.frame with rank and name columns

wt_wikispecies_parse returns a list

wt_wikispecies_search returns a list with slots for continue and query, where query holds the results, with query$search slot with the search results

References

https://www.mediawiki.org/wiki/API:Search for help on search

Examples

## Not run: 
# high level
wt_wikispecies(name = "Malus domestica")
wt_wikispecies(name = "Pinus contorta")
wt_wikispecies(name = "Ursus americanus")
wt_wikispecies(name = "Balaenoptera musculus")

# low level
pg <- wt_wiki_page("https://species.wikimedia.org/wiki/Abelmoschus")
wt_wikispecies_parse(pg)

# search wikispecies
# FIXME: utf=FALSE for now until curl::curl_escape fix 
# https://github.com/jeroen/curl/issues/228
wt_wikispecies_search(query = "pine tree", utf8=FALSE)

## use search results to dig into pages
res <- wt_wikispecies_search(query = "pine tree", utf8=FALSE)
lapply(res$query$search$title[1:3], wt_wikispecies)

## End(Not run)
## Not run: 
# high level
wt_wikispecies(name = "Malus domestica")
wt_wikispecies(name = "Pinus contorta")
wt_wikispecies(name = "Ursus americanus")
wt_wikispecies(name = "Balaenoptera musculus")

# low level
pg <- wt_wiki_page("https://species.wikimedia.org/wiki/Abelmoschus")
wt_wikispecies_parse(pg)

# search wikispecies
# FIXME: utf=FALSE for now until curl::curl_escape fix 
# https://github.com/jeroen/curl/issues/228
wt_wikispecies_search(query = "pine tree", utf8=FALSE)

## use search results to dig into pages
res <- wt_wikispecies_search(query = "pine tree", utf8=FALSE)
lapply(res$query$search$title[1:3], wt_wikispecies)

## End(Not run)

Package 'wikitaxa'

Help Index

wikitaxa

Description

Author(s)

List of Wikipedias

Description

Details

Wikidata taxonomy data

Description

Usage

Arguments

Details

Value

Examples

Get MediaWiki Page from API

Description

Usage

Arguments

Details

Value

See Also

Examples

Parse MediaWiki Page

Description

Usage

Arguments

Details

Value

See Also

Examples

Build MediaWiki Page URL

Description

Usage

Arguments

Value

See Also

Examples

Parse MediaWiki Page URL

Description

Usage

Arguments

Value

See Also

Examples

WikiCommons

Description

Usage

Arguments

Value

References

Examples

Wikipedia

Description

Usage

Arguments

Value

References

Examples

WikiSpecies

Description

Usage

Arguments

Value

References

Examples