Get Kew's Plants of the World code for a taxon
Get Kew's Plants of the World code for a taxon
get_pow( sci_com, accepted = FALSE, ask = TRUE, messages = TRUE, rows = NA, family_filter = NULL, rank_filter = NULL, x = NULL, ... ) as.pow(x, check = TRUE) ## S3 method for class 'pow' as.pow(x, check = TRUE) ## S3 method for class 'character' as.pow(x, check = TRUE) ## S3 method for class 'list' as.pow(x, check = TRUE) ## S3 method for class 'data.frame' as.pow(x, check = TRUE) ## S3 method for class 'pow' as.data.frame(x, ...) get_pow_(sci_com, messages = TRUE, rows = NA, x = NULL, ...)
sci_com |
character; A vector of common or scientific names. Or, a
|
accepted |
logical; If TRUE, removes names that are not accepted
valid names by ITIS. Set to |
ask |
logical; should |
messages |
logical; should progress be printed? |
rows |
numeric; Any number from 1 to infinity. If the default NA,
all rows are considered. Note that this function still only gives back
a pow class object with one to many identifiers. See
|
family_filter |
(character) A division (aka phylum) name to filter
data after retrieved from NCBI. Optional. See |
rank_filter |
(character) A taxonomic rank name to filter data after
retrieved from NCBI. See rank_ref for possible options.
Though note that some data sources use atypical ranks, so inspect the data
itself for options. Optional. See |
x |
For |
... |
Curl options passed on to crul::HttpClient |
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
The parameters family_filter anrank_filterer are not
used in the search to the data provider, but are used in filtering the data down to a
subset that is closer to the target you want. For these two parameters,
you can use regex strings since we use grep() internally to match.
Filtering narrows down to the set that matches your query, and removes the rest.
As of February 2019, KEW was limiting to 5 requests per second. Note that they may change that number in the future.
If you get errors that contain 429 you are hitting the rate limit, and you
can get around it by doing requests with Sys.sleep in between requests.
Other pow:
pow_lookup(),
pow_search(),
pow_synonyms()
Other taxonomic-ids:
get_boldid(),
get_eolid(),
get_gbifid(),
get_ids(),
get_iucn(),
get_natservid(),
get_nbnid(),
get_tolid(),
get_tpsid(),
get_tsn(),
get_uid(),
get_wiki(),
get_wormsid()
## Not run:
get_pow(sci_com="Helianthus")
get_pow(c("Helianthus","Quercus douglasii"))
# Get back a subset
get_pow(sci_com="Helianthus", rows = 1)
get_pow(sci_com="Helianthus", rows = 1:10)
# When not found
get_pow("howdy")
get_pow(c("Helianthus annuus", "howdy"))
# Narrow down results
# to accepted names
get_pow("Helianthus", accepted = TRUE)
# to a kingom
get_pow("Helianthus", rank_filter = "genus")
# to accepted names and rank
get_pow("Helianthus annuus", accepted = TRUE, rank_filter = "species")
# to a family
get_pow("flower", family_filter = "Acanthaceae")
# Convert a pow without class information to a pow class
z <- get_pow("Helianthus annuus", accepted = TRUE, rank_filter = "species")
# already a pow, returns the same
as.pow(z)
as.pow("urn:lsid:ipni.org:names:119003-2")
# character vector, length > 1
ids <- c("urn:lsid:ipni.org:names:119003-2","urn:lsid:ipni.org:names:328247-2")
as.pow(ids)
# list, with character strings
as.pow(as.list(ids))
## dont check, much faster
as.pow("urn:lsid:ipni.org:names:119003-2", check=FALSE)
as.pow(ids, check=FALSE)
as.pow(as.list(ids), check=FALSE)
(out <- as.pow(ids))
data.frame(out)
as.pow( data.frame(out) )
# Get all data back
get_pow_("Quercus", rows=1:5)
get_pow_("Quercus", rows=1)
get_pow_(c("Pinus", "Abies"), rows = 1:3)
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