taxize (version 0.9.4)

iucn_summary: Get a summary from the IUCN Red List

Description

Get a summary from the IUCN Red List (http://www.iucnredlist.org/).

Usage

iucn_summary(x, parallel = FALSE, distr_detail = FALSE, key = NULL, ...)
iucn_summary_id(species_id, silent = TRUE, parallel = FALSE,
  distr_detail = FALSE, ...)

Arguments

x

character; Scientific name. Should be cleaned and in the format <Genus> <Species>.

parallel

logical; Search in parallel to speed up search. You have to register a parallel backend if TRUE. See e.g., doMC, doSNOW, etc.

distr_detail

logical; If TRUE, the geographic distribution is returned as a list of vectors corresponding to the different range types: native, introduced, etc.

key

a Redlist API key, get one from http://apiv3.iucnredlist.org/api/v3/token Required for iucn_summary but not needed for iucn_summary_id. Defaults to NULL in case you have your key stored (see Redlist Authentication below).

...

Currently not used.

species_id

an IUCN ID

silent

logical; Make errors silent or not (when species not found).

Value

A list (for every species one entry) of lists with the following items:

status

Red List Category.

history

History of status, if available.

distr

Geographic distribution, if available.

trend

Trend of population size, if available.

Redlist Authentication

iucn_summary uses the new Redlist API for searching for a IUCN ID, so we use the rl_search function internally. This function requires an API key. Get the key at http://apiv3.iucnredlist.org/api/v3/token, and pass it to the key parameter, or store in your .Renviron file like IUCN_REDLIST_KEY=yourkey or in your .Rprofile file like options(iucn_redlist_key="yourkey". We strongly encourage you to not pass the key in the function call but rather store it in one of those two files. This key will also set you up to use the rredlist package.

Details

Beware: IUCN functions can give back incorrect data. This isn't our fault. We do our best to get you the correct data quickly, but sometimes IUCN gives back the wrong data, and sometimes Global Names gives back the wrong data. We will fix these as soon as possible. In the meantime, just make sure that the data you get back is correct.

iucn_summary has a default method that errors when anything's passed in that's not character or iucn class - a iucn_summary.character method for when you pass in taxon names - and a iucn_summary.iucn method so you can pass in iucn class objects as output from get_iucn or as.iucn. If you already have IUCN IDs, coerce them to iucn class via as.iucn(..., check = FALSE)

See Also

iucn_status

Examples

# NOT RUN {
# if you send a taxon name, an IUCN API key is required
## here, the key is being detected from a .Rprofile file
## or .Renviron file, See "Redlist Authentication" above
iucn_summary("Lutra lutra")

ia <- iucn_summary(c("Panthera uncia", "Lynx lynx"))
ia <- iucn_summary(c("Panthera uncia", "Lynx lynx", "aaa"))

## get detailed distribution
iac <- iucn_summary(x="Ara chloropterus", distr_detail = TRUE)
iac[[1]]$distr


# If you pass in an IUCN ID, you don't need to pass in a Redlist API Key
ia <- iucn_summary_id(c(22732, 12519))
# extract status
iucn_status(ia)
# extract other available information
ia[['Lynx lynx']]$history
ia[['Panthera uncia']]$distr
ia[[2]]$trend
## the outputs aren't quite identical, but we're working on it
identical(
  iucn_summary_id(c(22732, 12519)),
  iucn_summary(as.iucn(c(22732, 12519)))
)

# using parallel, e.g., with doMC package, register cores first
# library(doMC)
# registerDoMC(cores = 2)
# nms <- c("Panthera uncia", "Lynx lynx", "Ara chloropterus", "Lutra lutra")
# (res <- iucn_summary(nms, parallel = TRUE))
# }