R: Resolve names using Global Names Recognition and Discovery.

scrapenames {taxize} | R Documentation

## 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 `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 myrmecocystus@gmail.com

### Examples

    ## Not run:
    # Get data from a website using its URL
    scrapenames('http://en.wikipedia.org/wiki/Araneae')
    scrapenames('http://en.wikipedia.org/wiki/Animalia')
    scrapenames('http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0095068')
    scrapenames('http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080498')
    scrapenames('http://ucjeps.berkeley.edu/cgi-bin/get_JM_treatment.pl?CARYOPHYLLACEAE')

    # Scrape names from a pdf at a URL
    url <- 'http://www.plosone.org/article/fetchObject.action?uri=
    info%3Adoi%2F10.1371%2Fjournal.pone.0058268&representation=PDF'
    scrapenames(url = sub('\n', '', url))

    # With arguments
    scrapenames(url = 'http://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf',
      unique=TRUE)
    scrapenames(url = 'http://en.wikipedia.org/wiki/Araneae',
      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='http://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf',
      return_content = TRUE)

    # use curl options
    library("httr")
    scrapenames(text='A spider named Pardosa moesta Banks, 1892')

    ## End(Not run)

[Package taxize version 0.9.0 Index]