taxize (version 0.9.4)

get_natservid: Get NatureServe taxonomic ID for a taxon name

Description

Get NatureServe taxonomic ID for a taxon name

Usage

get_natservid(query, searchtype = "scientific", ask = TRUE,
  verbose = TRUE, rows = NA, key = NULL, ...)
as.natservid(x, check = TRUE)
# S3 method for natservid
as.natservid(x, check = TRUE)
# S3 method for character
as.natservid(x, check = TRUE)
# S3 method for list
as.natservid(x, check = TRUE)
# S3 method for numeric
as.natservid(x, check = TRUE)
# S3 method for data.frame
as.natservid(x, check = TRUE)
# S3 method for natservid
as.data.frame(x, ...)
get_natservid_(query, verbose = TRUE, rows = NA, key = NULL, ...)

Arguments

query

character; A vector of common or scientific names.

searchtype

character; One of 'scientific' (default) or 'common'. This doesn't affect the query to NatureServe - but rather affects what column of data is targeted in name filtering post data request.

ask

logical; should get_natservid be run in interactive mode? If TRUE and more than one wormsid is found for the species, the user is asked for input. If FALSE NA is returned for multiple matches.

verbose

logical; should progress be printed?

rows

numeric; Any number from 1 to infinity. If the default NaN, all rows are considered. Note that this function still only gives back a natservid class object with one to many identifiers. See get_natservid_ to get back all, or a subset, of the raw data that you are presented during the ask process.

key

(character) your NatureServe API key. Required. See Authentication below for more.

...

Ignored

x

Input to as.natservid

check

logical; Check if ID matches any existing on the DB, only used in as.natservid

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

Get an API key from NatureServe at https://services.natureserve.org/developer/index.jsp. You can pass your token in as an argument or store it one of two places:

• your .Rprofile file with an entry like options(NatureServeKey = "your-natureserve-key")

• your .Renviron file with an entry like NATURE_SERVE_KEY=your-natureserve-key

See Startup for information on how to create/find your .Rprofile and .Renviron files

See Also

classification

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

Examples

# NOT RUN {
(x <- get_natservid("Helianthus annuus"))
attributes(x)
attr(x, "match")
attr(x, "multiple_matches")
attr(x, "pattern_match")
attr(x, "uri")

get_natservid('Gadus morhua')
get_natservid(c("Helianthus annuus", 'Gadus morhua'))

# specify rows to limit choices available
get_natservid('Ruby Quaker Moth', 'common')
get_natservid('Ruby*', 'common')
get_natservid('Ruby*', 'common', rows=1)
get_natservid('Ruby*', 'common', rows=1:2)

# When not found
get_natservid("howdy")
get_natservid(c('Gadus morhua', "howdy"))

# Convert a natservid without class information to a natservid class
# already a natservid, returns the same
as.natservid(get_natservid('Gadus morhua'))
# same
as.natservid(get_natservid(c('Gadus morhua', 'Pomatomus saltatrix')))
# character
as.natservid("ELEMENT_GLOBAL.2.101905")
# character vector, length > 1
as.natservid(c("ELEMENT_GLOBAL.2.101905", "ELEMENT_GLOBAL.2.101998"))
# list, either numeric or character
as.natservid(list("ELEMENT_GLOBAL.2.101905", "ELEMENT_GLOBAL.2.101998"))
## dont check, much faster
as.natservid("ELEMENT_GLOBAL.2.101905", check = FALSE)
as.natservid(c("ELEMENT_GLOBAL.2.101905", "ELEMENT_GLOBAL.2.101998"),
  check = FALSE)
as.natservid(list("ELEMENT_GLOBAL.2.101905", "ELEMENT_GLOBAL.2.101998"),
  check = FALSE)

(out <- as.natservid(
  c("ELEMENT_GLOBAL.2.101905", "ELEMENT_GLOBAL.2.101998")))
data.frame(out)
as.natservid( data.frame(out) )

# Get all data back
get_natservid_("Ruby*")
get_natservid_("Ruby*", rows=1:3)
# }