scrapenames {taxize}

Resolve names using Global Names Recognition and Discovery.

Description

Uses the Global Names Recognition and Discovery service, see http://gnrd.globalnames.org/

Note: this function sometimes gives data back and sometimes not. The API that this function is extremely buggy.

Usage

scrapenames(
  url = NULL,
  file = NULL,
  text = NULL,
  engine = NULL,
  unique = NULL,
  verbatim = NULL,
  detect_language = NULL,
  all_data_sources = NULL,
  data_source_ids = NULL,
  return_content = FALSE,
  ...
)

Arguments

url

An encoded URL for a web page, PDF, Microsoft Office document, or image file, see examples

file

When using multipart/form-data as the content-type, a file may be sent. This should be a path to your file on your machine.

text

Type: string. Text content; best used with a POST request, see examples

engine

(optional) (integer) Default: 0. Either 1 for TaxonFinder, 2 for NetiNeti, or 0 for both. If absent, both engines are used.

unique

(optional) (logical) If TRUE (default), response has unique names without offsets.

verbatim

(optional) Type: boolean, If TRUE (default to FALSE), response excludes verbatim strings.

detect_language

(optional) Type: boolean, When TRUE (default), NetiNeti is not used if the language of incoming text is determined not to be English. When FALSE, NetiNeti will be used if requested.

all_data_sources

(optional) Type: boolean. Resolve found names against all available Data Sources.

data_source_ids

(optional) Type: string. Pipe separated list of data source ids to resolve found names against. See list of Data Sources http://resolver.globalnames.org/data_sources

return_content

(logical) return OCR'ed text. returns text string in x$meta$content slot. Default: FALSE

...

Further args passed to crul::verb-GET

Details

One of url, file, or text must be specified - and only one of them.

Value

A list of length two, first is metadata, second is the data as a data.frame.

Author(s)

Scott Chamberlain

Examples

## Not run: 
# Get data from a website using its URL
scrapenames('https://en.wikipedia.org/wiki/Spider')
scrapenames('https://en.wikipedia.org/wiki/Animal')
scrapenames('https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0095068')
scrapenames('https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080498')
scrapenames('http://ucjeps.berkeley.edu/cgi-bin/get_JM_treatment.pl?CARYOPHYLLACEAE')

# Scrape names from a pdf at a URL
url <- 'https://journals.plos.org/plosone/article/file?id=
10.1371/journal.pone.0058268&type=printable'
scrapenames(url = sub('\n', '', url))

# With arguments
scrapenames(url = 'https://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf',
  unique=TRUE)
scrapenames(url = 'https://en.wikipedia.org/wiki/Spider',
  data_source_ids=c(1, 169))

# Get data from a file
speciesfile <- system.file("examples", "species.txt", package = "taxize")
scrapenames(file = speciesfile)

nms <- paste0(names_list("species"), collapse="\n")
file <- tempfile(fileext = ".txt")
writeLines(nms, file)
scrapenames(file = file)

# Get data from text string
scrapenames(text='A spider named Pardosa moesta Banks, 1892')

# return OCR content
scrapenames(url='https://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf',
  return_content = TRUE)

## End(Not run)