taxize (version 0.10.0)

scrapenames: Find taxon 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 using is extremely buggy.

Usage

scrapenames(
  url = NULL,
  text = NULL,
  format = "csv",
  bytes_offset = FALSE,
  return_content = FALSE,
  unique_names = TRUE,
  ambiguous_names = FALSE,
  no_bayes = FALSE,
  odds_details = FALSE,
  language = "detect",
  words_around = 0,
  verification = TRUE,
  sources = NULL,
  all_matches = FALSE,
  ...,
  file = NULL,
  unique = NULL,
  engine = NULL,
  detect_language = NULL,
  data_source_ids = NULL
)

Value

A tibble::tibble() or list representing parsed JSON output depending on the value of the format option.

Arguments

url

(character) If text parameter is empty, and url is given, GNfinder will process the URL and will find names in the content of its body.

text

(character) Contains the text which will be checked for scientific names. If this parameter is not empty, the url parameter is ignored.

format

(character) Sets the output format. It can be set to: "csv" (the default), "tsv", or "json".

bytes_offset

(logical) This changes how the position of a detected name in text is calculated. Normally a name's start and end positions are given as the number of UTF-8 characters from the beginning of the text. If this is TRUE, the start and end offsets are recalculated in the number of bytes.

return_content

(logical) If this is TRUE, the text used for the name detection is returned back. This is especially useful if the input was not a plain UTF-8 text and had to be prepared for name-finding. Then the returned content can be used together with start and end fields of detected name-strings to locate the strings in the text.

unique_names

(logical) If this is TRUE, the output returns a list of unique names, instead of a list of all name occurrences. Unique list of names does not provide position information of a name in the text.

ambiguous_names

(logical) If this is TRUE, strings which are simultaneously scientific names and "normal" words are not filtered out from the results. For example, generic names like America, Cancer, Cafeteria will be returned in the results.

no_bayes

(logical) If this is TRUE, only heuristic algorithms are used for name detection.

odds_details

(logical) If TRUE, the result will contain odds of all features used for calculation of NaiveBayes odds. Odds describe probability of a name to be 'real'. The higher the odds, the higher the probability that a detected name is not a false positive. Odds are calculated by multiplication of the odds of separate features. Odds details explain how the final odds value is calculated.

language

(character) The language of the text. Language value is used for calculation of Bayesian odds. If this parameter is not given, "eng" is used by default. Currently only English and German languages are supported. Valid values are: "eng", "deu", and "detect".

words_around

(integer) Allows to see the context surrounding a name-string. This sets the number of words located immediately before or after a detected name. These words are then returned in the output. Default is 0, maximum value is 5.

verification

(character) When this TRUE, there is an additional verification step for detected names. This step requires internet connection and uses https://verifier.globalnames.org/api/v1 for verification queries.

sources

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

all_matches

When this option is true all found results are returned, not only the bestResults. The bestResult field in this case is null, and results field should contain found results of the matches.

...

Further args passed to crul::verb-GET

file

Defunct. If you feel this is important functionality submit an issue at "https://github.com/ropensci/taxize"

unique

Defunct. See the unique_names option.

engine

Defunct. The API used no longer supports this option.

detect_language

Defunct. See the language option.

data_source_ids

Defunct. See the sources option.

Author

Scott Chamberlain, Zachary Foster

Examples

if (FALSE) {
# 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(url = 'https://en.wikipedia.org/wiki/Spider', source=c(1, 169))

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

# return OCR content
scrapenames(text='A spider named Pardosa moesta Banks, 1892',
            return_content = TRUE, format = 'json')
}