originr (version 0.4.0)

eol: Search for presence of taxonomic names in EOL invasive species databases.

Description

See Details for important information.

Usage

eol(
  name,
  dataset = "all",
  searchby = grep,
  page = NULL,
  per_page = 500,
  key = NULL,
  messages = TRUE,
  count = FALSE,
  ...
)
eol_invasive_data(...)

Arguments

name

A taxonomic name, or a vector of names.

dataset

One of all, gisd100, gisd, isc, daisie, i3n, or mineps. See the Details for what each dataset ID.

searchby

One of 'grep' (exact match) or 'agrep' (fuzzy match)

page

A maximum of 30 results are returned per page. This parameter allows you to fetch more pages of results if there are more than 30 matches (Default: 1)

per_page

Results to get per page. Default: 500

key

Your EOL API key; loads from .Rprofile.

messages

(logical) If TRUE the actual taxon queried is printed on the console.

count

(logical) If TRUE, give back a count of number of taxa listed as invasive, if FALSE (default), the normal output is given.

...

curl options passed on to HttpClient

Value

A list of data.frame's/strings with results, with each element named by the input elements to the name parameter.

Details

eol_invasive_data() gives you the entire data.frame from the "dataset=all", while eol() let's you search on a vector of names against any of the datasets

IMPORTANT: note that setting dataset="all" will give you surprising results. EOL does not include informaiton on which of the invasive datasets (i.e., gisd100, gisd, isc, daisie, i3n, or mineps) the taxon is found in, and sometimes e.g., if taxon X is in GISD, you might not find it in "all", weird. I don't know why that's happening, but it shouldn't happen.

IMPORTANT: When you get a returned NaN for a taxon, that means it's not on the invasive list in question. If the taxon is found, a taxon identifier is returned.

Beware that some datasets are quite large, and may take 30 sec to a minute to pull down all data before we can search for your species. Note there is no parameter in this API method for searching by taxon name.

eol() is vectorized, so you can pass a single name or a vector of names.

It's possible to return JSON or XML with the EOL API. However, this function only returns JSON.

Options for the dataset parameter are

• all - All datasets

• gisd100 - 100 of the World's Worst Invasive Alien Species (Global Invasive Species Database) https://eol.org/resources/477

• gisd - Global Invasive Species Database 2013 http://eol.org/collections/54983

• isc - Centre for Agriculture and Biosciences International Invasive Species Compendium (ISC) http://eol.org/collections/55180

• daisie - Delivering Alien Invasive Species Inventories for Europe (DAISIE) Species List http://eol.org/collections/55179

• i3n - IABIN Invasives Information Network (I3N) Species http://eol.org/collections/55176

• mineps - Marine Invaders of the NE Pacific Species http://eol.org/collections/55331

Datasets are not updated that often. Here's last updated dates for some of the datasets as of 2014-08-25

• gisd100 updated 6 mos ago

• gisd updated 1 yr ago

• isc updated 1 yr ago

• daisie updated 1 yr ago

• i3n updated 1 yr ago

• mineps updated 1 yr ago

Examples

# NOT RUN {
eol(name='Brassica oleracea', dataset='gisd')
eol(name=c('Lymantria dispar','Cygnus olor','Hydrilla verticillata',
  'Pinus concolor'), dataset='gisd')
eol(name='Sargassum', dataset='gisd')
eol(name='Ciona intestinalis', dataset='mineps')
eol(name=c('Lymantria dispar','Cygnus olor','Hydrilla verticillata',
  'Pinus concolor'), dataset='i3n')
eol(name=c('Branta canadensis','Gallus gallus','Myiopsitta monachus'),
   dataset='daisie')
eol(name=c('Branta canadensis','Gallus gallus','Myiopsitta monachus'),
  dataset='isc')

# Count
eol(name=c('Lymantria dispar','Cygnus olor','Hydrilla verticillata',
  'Pinus concolor'), dataset='gisd', count = TRUE)

# curl options
eol(name='Sargassum', dataset='gisd', verbose = TRUE)
# }