Get NatureServe taxonomic ID for a taxon name
get_natservid(
sci_com,
searchtype = "scientific",
ask = TRUE,
messages = TRUE,
rows = NA,
query = 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_(
sci_com,
searchtype = "scientific",
messages = TRUE,
rows = NA,
query = NULL,
...
)
character; A vector of common or scientific names. Or, a
taxon_state
object (see taxon-state)
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.
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. default: TRUE
logical; should progress be printed? default: TRUE
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.
Deprecated, see sci_com
curl options passed on to crul::verb-POST
Input to as.natservid
logical; Check if ID matches any existing on the DB, only
used in as.natservid()
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 no longer required
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wiki()
,
get_wormsid()
if (FALSE) {
(x <- get_natservid("Helianthus annuus", verbose = TRUE))
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('Pomatomus saltatrix'))
# same
as.natservid(get_natservid(c('Gadus morhua', 'Pomatomus saltatrix')))
# character
as.natservid(101905)
# character vector, length > 1
as.natservid(c(101905, 101998))
# list, either numeric or character
as.natservid(list(101905, 101998))
## dont check, much faster
as.natservid(101905, check = FALSE)
as.natservid(c(101905, 101998), check = FALSE)
as.natservid(list(101905, 101998), check = FALSE)
(out <- as.natservid(c(101905, 101998), check = FALSE))
data.frame(out)
as.natservid( data.frame(out) )
# Get all data back
get_natservid_("Helianthus")
get_natservid_("Ruby*", searchtype = "common")
get_natservid_("Ruby*", searchtype = "common", rows=1:3)
}