taxize (version 0.5.2)

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, verbose = TRUE, key = NULL, rows = NA,
  ...)
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_(sciname, verbose = 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.

verbose

logical; If TRUE the actual taxon queried is printed on the console.

key

API key

rows

numeric; Any number from 1 to inifity. 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

...

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 unique identifiers (EOL). If a taxon is not found NA. If more than one ID is found the function asks for user input.

See Also

get_tsn, get_uid, get_tpsid

Examples

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
as.eolid(get_eolid("Chironomus riparius")) # already a eolid, returns the same
as.eolid(get_eolid(c("Chironomus riparius","Pinus contorta"))) # same
as.eolid(24954444) # numeric
as.eolid(c(24954444,51389511,57266265)) # numeric vector, length > 1
as.eolid("24954444") # character
as.eolid(c("24954444","51389511","57266265")) # character vector, length > 1
as.eolid(list("24954444","51389511","57266265")) # list, either numeric or character
## 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"))