resolve_phylopic: Use a taxonomic name from another database to get a PhyloPic...

In sckott/rphylopic: Get Silhouettes of Organisms from PhyloPic

Use a taxonomic name from another database to get a PhyloPic image UUID

Description

This function takes a supplied taxonomic name, queries it via the specified external API, resolves the API's returned taxonomic ID to the PhyloPic taxonomic node database, then retrieves PhyloPic image uuids (or urls) for that node.

Usage

resolve_phylopic(
  name,
  api = "gbif.org",
  hierarchy = FALSE,
  max_ranks = 5,
  n = 1,
  filter = NULL,
  url = FALSE
)

Arguments

name	character. A full or partial taxonomic name to be queried via the specified api.
api	character. The API in which to query name. See Details for the available options.
hierarchy	logical. Whether the taxonomic hierarchy of name should be retrieved from the API and used to get several sets of PhyloPic image uuids (or urls).
max_ranks	numeric. The maximum number of taxonomic ranks that should be included if hierarchy is TRUE.
n	numeric. How many uuids should be returned? Depending on the requested name, multiple silhouettes might exist. If n exceeds the number of available images, all available uuids will be returned. This argument defaults to 1.
filter	character. Filter uuid(s) by usage license. Use "by" to limit results to image uuids which do not require attribution, "nc" for image uuids which allow commercial usage, and "sa" for image uuids without a ShareAlike clause. The user can also combine these filters as a vector.
url	logical. If FALSE (default), only the uuid is returned. If TRUE, a valid PhyloPic image url of the uuid is returned.

Details

If hierarchy is FALSE, the specified name is queried via the specified api. The matched id is then resolved to the matching taxonomic node in the PhyloPic database. If hierarchy is TRUE, the full taxonomic hierarchy for name is retrieved from the specified api, those taxonomic names are subset to max_ranks ranks (starting from the specified name and ascending the hierarchy). Then each of those names is resolved to the matching taxonomic node in the PhyloPic database (where possible). In either case, get_uuid() is then used to retrieve n image UUID(s) for each taxonomic name.

Note that while the names of the returned list are the taxonomic names as reported by the specified api, the PhyloPic images that are returned are associated with whatever taxonomic node that taxonomic name resolves to in the PhyloPic database. This means that, if hierarchy is TRUE, the same images may be returned for multiple taxonomic names. Also, if a particular taxonomic name does not resolve to any node in the PhyloPic database, no images will be returned for that name.

The following APIs are available for querying (api):

• "eol.org": the Encyclopedia of Life (note: hierarchy = TRUE is not currently available for this API) ("eol" is also allowed)

• "gbif.org": the Global Biodiversity Information Facility ("gbif" is also allowed)

• "marinespecies.org": the World Registor of Marine Species ("worms" is also allowed)

• "opentreeoflife.org": the Open Tree of Life ("otol" is also allowed)

• "paleobiodb.org": the Paleobiology Database ("pbdb" is also allowed)

Value

A list where each value is n (or fewer) PhyloPic image uuids (or urls if url = TRUE) and each name is the taxonomic name as matched and reported by the specified api. If hierarchy is FALSE, the list has length 1. If hierarchy is TRUE, the list has maximum length max_ranks.

Examples

## Not run: 
# get a uuid for a single name
resolve_phylopic(name = "Canis lupus")
# get uuids for the taxonomic hierarchy
resolve_phylopic(name = "Velociraptor mongoliensis", api = "paleobiodb.org",
                 hierarchy = TRUE, max_ranks = 3)

## End(Not run)

sckott/rphylopic documentation built on May 1, 2024, 12:04 a.m.