| get_natservid {taxize} | R Documentation |
Get NatureServe taxonomic ID for a taxon name
get_natservid(query, searchtype = "scientific", ask = TRUE, verbose = TRUE, rows = NA, key = NULL, ...) as.natservid(x, check = TRUE) ## S3 method for class 'natservid' as.natservid(x, check = TRUE) ## S3 method for class 'character' as.natservid(x, check = TRUE) ## S3 method for class 'list' as.natservid(x, check = TRUE) ## S3 method for class 'numeric' as.natservid(x, check = TRUE) ## S3 method for class 'data.frame' as.natservid(x, check = TRUE) ## S3 method for class 'natservid' as.data.frame(x, ...) get_natservid_(query, verbose = TRUE, rows = NA, key = NULL, ...)
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 |
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
|
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 |
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
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
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
## 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)
## End(Not run)