Get NatureServe taxonomic ID for a taxon name
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 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_( sci_com, searchtype = "scientific", messages = TRUE, rows = NA, query = NULL, ... )
sci_com |
character; A vector of common or scientific names. Or, a
|
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 |
messages |
logical; should progress be printed? default: |
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
|
query |
Deprecated, see |
... |
curl options passed on to crul::verb-POST |
x |
Input to |
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
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()
## Not run:
(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)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.