taxize (version 0.9.4)

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(sciname, ask = TRUE, messages = TRUE, key = NULL, rows = NA,
  ...)
as.eolid(x, check = TRUE)
# S3 method for eolid
as.eolid(x, check = TRUE)
# S3 method for character
as.eolid(x, check = TRUE)
# S3 method for list
as.eolid(x, check = TRUE)
# S3 method for numeric
as.eolid(x, check = TRUE)
# S3 method for data.frame
as.eolid(x, check = TRUE)
# S3 method for eolid
as.data.frame(x, ...)
get_eolid_(sciname, messages = TRUE, key = NULL, rows = NA, ...)

Arguments

sciname

character; scientific name.

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.

key

API key. passed on to eol_search and eol_pages internally

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.

...

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

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

Authentication

See taxize-authentication for help on authentication

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.

See Also

classification

Other taxonomic-ids: get_boldid, get_colid, get_gbifid, get_ids, get_iucn, get_natservid, get_nbnid, get_tolid, get_tpsid, get_tsn, get_uid, get_wiki, get_wormsid

Examples

# NOT RUN {
get_eolid(sciname='Pinus contorta')
get_eolid(sciname='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(sciname="uaudnadndj")
get_eolid(c("Chironomus riparius", "uaudnadndj"))

# 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(24954444)
# numeric vector, length > 1
as.eolid(c(24954444,51389511,57266265))
# character
as.eolid("24954444")
# character vector, length > 1
as.eolid(c("24954444","51389511","57266265"))
# list, either numeric or character
as.eolid(list("24954444","51389511","57266265"))
## dont check, much faster
as.eolid("24954444", check=FALSE)
as.eolid(24954444, check=FALSE)
as.eolid(c("24954444","51389511","57266265"), check=FALSE)
as.eolid(list("24954444","51389511","57266265"), check=FALSE)

(out <- as.eolid(c(24954444,51389511,57266265)))
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"))
# }