Get Kew's Plants of the World code for a taxon

Get Kew's Plants of the World code for a taxon

Usage

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 pow
as.pow(x, check = TRUE)

# S3 method for character
as.pow(x, check = TRUE)

# S3 method for list
as.pow(x, check = TRUE)

# S3 method for data.frame
as.pow(x, check = TRUE)

# S3 method for pow
as.data.frame(x, ...)

get_pow_(sci_com, messages = TRUE, rows = NA, x = NULL, ...)

Arguments

sci_com

character; A vector of common or scientific names. Or, a taxon_state object (see taxon-state)

accepted

logical; If TRUE, removes names that are not accepted valid names by ITIS. Set to FALSE (default) to give back both accepted and unaccepted names.

ask

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

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 get_pow_() to get back all, or a subset, of the raw data that you are presented during the ask process.

family_filter

(character) A division (aka phylum) name to filter data after retrieved from NCBI. Optional. See Filtering below.

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 Filtering below.

x

For get_pow(): deprecated, see sci_com. For as.pow, various, see examples

...

Curl options passed on to crul::HttpClient

check

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

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

Filtering

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.

Rate-limits

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.

See also

classification()

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()

Examples

if (FALSE) {
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)
}