rgbif: Interface to the Global 'Biodiversity' Information Facility 'API'

GBIFが提供するAPIのR用インターフェース

> library(rgbif)

バージョン: 0.9.0

関数名 概略
check_wkt Check input WKT
count_facet Facetted count occurrence search.
dataset_metrics Get details on a GBIF dataset.
dataset_search Search datasets in GBIF.
dataset_suggest Suggest datasets in GBIF.
datasets Search for datasets and dataset metadata.
downloads Downloads interface
elevation Get elevation for lat/long points from a data.frame or list of points.
enumeration Enumerations.
gbif_bbox2wkt Convert a bounding box to a Well Known Text polygon, and a WKT to a bounding box
gbif_citation Get citation for datasets used
gbif_issues Table of GBIF issues, with codes used in data output, full issue name, and descriptions.
gbif_names View highlighted terms in name results from GBIF.
gbif_oai GBIF registry data via OAI-PMH
gbif_photos View photos from GBIF.
gbifmap Make a map to visualize GBIF occurrence data.
installations Installations metadata.
isocodes Table of country two character ISO codes, and GBIF names
name_backbone Lookup names in the GBIF backbone taxonomy.
name_lookup Lookup names in all taxonomies in GBIF.
name_suggest A quick and simple autocomplete service that returns up to 20 name usages by doing prefix matching against the scientific name. Results are ordered by relevance.
name_usage Lookup details for specific names in all taxonomies in GBIF.
networks Networks metadata.
nodes Nodes metadata.
occ_count Get number of occurrence records.
occ_download Spin up a download request for GBIF occurrence data.
occ_download_cancel Cancel a download cretion process.
occ_download_get Get a download from GBIF.
occ_download_import Import a downloaded file from GBIF.
occ_download_list Lists the downloads created by a user.
occ_download_meta Retrieves the occurrence download metadata by its unique key.
occ_fields Vector of fields in the output for the function 'occ_search'
occ_get Get data for specific GBIF occurrences.
occ_issues Parse and examine further GBIF issues on a dataset.
occ_issues_lookup Lookup occurrence issue definitions and short codes
occ_metadata Search for catalog numbers, collection codes, collector names, and institution codes.
occ_search Search for GBIF occurrences.
organizations Organizations metadata.
parsenames Parse taxon names using the GBIF name parser.
read_wkt Check input WKT
rgb_country_codes Look up 2 character ISO country codes
rgbif-defunct Defunct functions in rgbif
rgbif-package Interface to the Global Biodiversity Information Facility API.
taxrank Get the possible values to be used for (taxonomic) rank arguments in GBIF API methods.
typestatus Type status options for GBIF searching

isocodes

> isocodes %>% head()

  code                 name            gbif_name
1   AD              Andorra              ANDORRA
2   AE United Arab Emirates UNITED_ARAB_EMIRATES
3   AF          Afghanistan          AFGHANISTAN
4   AG  Antigua and Barbuda      ANTIGUA_BARBUDA
5   AI             Anguilla             ANGUILLA
6   AL              Albania              ALBANIA

name_suggest

Arguments

  • q
  • datasetKey
  • rank... 分類階級
  • fields
  • start
  • limit
  • ...
> name_suggest(q = "Quercus acuta")
> name_suggest(q = "Quercus", rank = "genus")

occ_count

> occ_count(taxonKey = NULL, georeferenced = NULL, basisOfRecord = NULL,
+   datasetKey = NULL, date = NULL, catalogNumber = NULL, country = NULL,
+   hostCountry = NULL, year = NULL, from = 2000, to = 2012,
+   type = "count", publishingCountry = "US", nubKey = NULL,
+   protocol = NULL, ...)

occ_search

GBIF生物情報からの検索

Arguments

  • taxonKey
  • scientificName
  • country
  • publishingCountry
  • hasCoordinate
  • typeStatus
  • recordNumber
  • lastInterpreted
  • continent
  • geometry
  • recordedBy
  • basisOfRecord
  • datasetKey
  • eventDate
  • catalogNumber
  • year
  • month
  • decimalLatitude
  • decimalLongitude
  • elevation
  • depth
  • institutionCode
  • collectionCode
  • hasGeospatialIssue
  • issue
  • search
  • mediatype
  • limit
  • start
  • fields
  • return
  • ...
  • x
  • n
> occ_search

parsenames

> parsenames(scientificname = "x Agropogon littoralis")

          scientificName       type genusOrAbove specificEpithet   notho
1 x Agropogon littoralis SCIENTIFIC    Agropogon      littoralis GENERIC
  authorsParsed        canonicalName canonicalNameWithMarker
1          TRUE Agropogon littoralis   ×Agropogon littoralis
  canonicalNameComplete
1 ×Agropogon littoralis

taxrank

> taxrank()

[1] "kingdom"       "phylum"        "class"         "order"        
[5] "family"        "genus"         "species"       "infraspecific"