taxize: get_eolid – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

get_eolid

Get the EOL ID from Encyclopedia of Life from taxonomic names.

Description

Note that EOL doesn't expose an API endpoint for directly querying for EOL taxon ID's, so we first use the function eol_search() to find pages that deal with the species of interest, then use eol_pages() to find the actual taxon IDs.

Usage

get_eolid(
  sci_com,
  ask = TRUE,
  messages = TRUE,
  rows = NA,
  rank = NULL,
  data_source = NULL,
  sciname = NULL,
  ...
)

as.eolid(x, check = TRUE)

## S3 method for class 'eolid'
as.eolid(x, check = TRUE)

## S3 method for class 'character'
as.eolid(x, check = TRUE)

## S3 method for class 'list'
as.eolid(x, check = TRUE)

## S3 method for class 'numeric'
as.eolid(x, check = TRUE)

## S3 method for class 'data.frame'
as.eolid(x, check = TRUE)

## S3 method for class 'eolid'
as.data.frame(x, ...)

get_eolid_(sci_com, messages = TRUE, rows = NA, sciname = NULL, ...)

Arguments

`sci_com`	character; one or more scientific or common names. Or, a `taxon_state` object (see taxon-state)
`ask`	logical; should get_eolid be run in interactive mode? If TRUE and more than one ID is found for the species, the user is asked for input. If FALSE NA is returned for multiple matches.
`messages`	logical; If `TRUE` the actual taxon queried is printed on the console.
`rows`	numeric; Any number from 1 to infinity. If the default NA, all rows are considered. Note that this function still only gives back a eolid class object with one to many identifiers. See `get_eolid_()` to get back all, or a subset, of the raw data that you are presented during the ask process.
`rank`	(character) A taxonomic rank name. See rank_ref for possible options. Though note that some data sources use atypical ranks, so inspect the data itself for options. Optional. See `Filtering` below.
`data_source`	(character) A data source inside of EOL. These are longish names like e.g., "Barcode of Life Data Systems" or "USDA PLANTS images". Optional. See `Filtering` below.
`sciname`	Deprecated, see `sci_com`
`...`	Further args passed on to `eol_search()`
`x`	Input to `as.eolid()`
`check`	logical; Check if ID matches any existing on the DB, only used in `as.eolid()`

Details

EOL is a bit odd in that they have page IDs for each taxon, but then within that, they have taxon ids for various taxa within that page (e.g., GBIF and NCBI each have a taxon they refer to within the page [i.e., taxon]). And we need the taxon ids from a particular data provider (e.g, NCBI) to do other things, like get a higher classification tree. However, humans want the page id, not the taxon id. So, the id returned from this function is the taxon id, not the page id. You can get the page id for a taxon by using eol_search() and 'eol_pages(), and the URI returned in the attributes for a taxon will lead you to the taxon page, and the ID in the URL is the page id.

Value

A vector of taxonomic identifiers as an S3 class. If a taxon is not found an NA is given. If more than one identifier is found the function asks for user input if ask = TRUE, otherwise returns NA. If ask=FALSE and rows does not equal NA, then a data.frame is given back, but not of the uid class, which you can't pass on to other functions as you normally can.

See get_id_details for further details including attributes and exceptions

Filtering

The parameters rank and data_source are not used in the search to the data provider, but are used in filtering the data down to a subset that is closer to the target you want. For all these parameters, you can use regex strings since we use grep() internally to match. Filtering narrows down to the set that matches your query, and removes the rest.

Author(s)

Scott Chamberlain

Examples

## Not run: 
get_eolid(sci_com='Pinus contorta')
get_eolid(sci_com='Puma concolor')

get_eolid(c("Puma concolor", "Pinus contorta"))

# specify rows to limit choices available
get_eolid('Poa annua')
get_eolid('Poa annua', rows=1)
get_eolid('Poa annua', rows=2)
get_eolid('Poa annua', rows=1:2)

# When not found
get_eolid(sci_com="uaudnadndj")
get_eolid(c("Chironomus riparius", "uaudnadndj"))

# filter results to a rank or data source, or both
get_eolid("Satyrium")
get_eolid("Satyrium", rank = "genus")
get_eolid("Satyrium", data_source = "INAT")
get_eolid("Satyrium", rank = "genus",
  data_source = "North Pacific Species List")

# Convert a eolid without class information to a eolid class
# already a eolid, returns the same
as.eolid(get_eolid("Chironomus riparius"))
# same
as.eolid(get_eolid(c("Chironomus riparius","Pinus contorta")))
# numeric
as.eolid(10247706)
# numeric vector, length > 1
as.eolid(c(6985636,12188704,10247706))
# character
as.eolid("6985636")
# character vector, length > 1
as.eolid(c("6985636","12188704","10247706"))
# list, either numeric or character
as.eolid(list("6985636","12188704","10247706"))
## dont check, much faster
as.eolid("6985636", check=FALSE)
as.eolid(6985636, check=FALSE)
as.eolid(c("6985636","12188704","10247706"), check=FALSE)
as.eolid(list("6985636","12188704","10247706"), check=FALSE)

(out <- as.eolid(c(6985636,12188704,10247706)))
data.frame(out)
as.eolid( data.frame(out) )

# Get all data back
get_eolid_("Poa annua")
get_eolid_("Poa annua", rows=2)
get_eolid_("Poa annua", rows=1:2)
get_eolid_(c("asdfadfasd", "Pinus contorta"))

## End(Not run)

taxize

Taxonomic Information from Around the Web

v0.9.100

MIT + file LICENSE

Authors

Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Eduard Szoecs [aut], Zachary Foster [aut, cre], Zebulun Arendsee [aut], Carl Boettiger [ctb], Karthik Ram [ctb], Ignasi Bartomeus [ctb], John Baumgartner [ctb], James O'Donnell [ctb], Jari Oksanen [ctb], Bastian Greshake Tzovaras [ctb], Philippe Marchand [ctb], Vinh Tran [ctb], Maëlle Salmon [ctb], Gaopeng Li [ctb], Matthias Grenié [ctb], rOpenSci [fnd] (https://ropensci.org/)

Initial release