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rgbif (version 0.9.2)

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

Description

A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility ('GBIF'). 'GBIF' is a database of species occurrence records from sources all over the globe. 'rgbif' includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, and getting counts of occurrence records.

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Version

Install

install.packages('rgbif')

Monthly Downloads

7,110

Version

0.9.2

License

MIT + file LICENSE

Issues

32

Pull Requests

2

Stars

165

Forks

51

Maintainer

Scott Chamberlain

Last Published

February 2nd, 2016

Functions in rgbif (0.9.2)

%>%

Pipe operator
occ_get

Get data for specific GBIF occurrences.
gbif_photos

View photos from GBIF.
occ_download_get

Get a download from GBIF.
dataset_suggest

Suggest datasets in GBIF.
dataset_metrics

Get details on a GBIF dataset.
blanktheme

Custom ggplot2 theme
densitylist

The density web service provides access to records showing the density of occurrence records from the GBIF Network by one-degree cell.
density_spplist

The density web service provides access to records showing the density of occurrence records from the GBIF Network by one-degree cell.
check_wkt

Check input WKT
occ_count

Get number of occurrence records.
create_gist

Function that takes a list of files and creates payload for API
gbif_oai

GBIF registry data via OAI-PMH
name_lookup

Lookup names in all taxonomies in GBIF.
gbif_names

View highlighted terms in name results from GBIF.
occ_download_list

Lists the downloads created by a user.
isocodes

Table of country two character ISO codes, and GBIF names
count_facet

Facetted count occurrence search.
dataset_search

Search datasets in GBIF.
datasets

Search for datasets and dataset metadata.
gbif_bbox2wkt

Convert a bounding box to a Well Known Text polygon, and a WKT to a bounding box
gbif_issues

Table of GBIF issues, with codes used in data output, full issue name, and descriptions.
gbifdata

Get data.frame from occurrencelist, occurrencelist_many, or densitylist.
elevation

Get elevation for lat/long points from a data.frame or list of points.
installations

Installations metadata.
occ_data

Search for GBIF occurrences - simplified for speed
name_usage

Lookup details for specific names in all taxonomies in GBIF.
gbif_citation

Get citation for datasets used
nodes

Nodes metadata.
occ_metadata

Search for catalog numbers, collection codes, collector names, and institution codes.
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.
gist

Post a file as a Github gist
networks

Networks metadata.
occ_fields

Vector of fields in the output for the function occ_search
occurrencecount

Counts taxon concept records matching a range of filters.
gbifmap_dens

Make a simple map to visualize GBIF data density data
gbifmap_list

Make a simple map to visualize GBIF point data.
get_credentials

Get Github credentials from use in console
gbifmap

Make a map to visualize GBIF occurrence data.
occ_search

Search for GBIF occurrences
occ_download_cancel

Cancel a download cretion process.
occ_download

Spin up a download request for GBIF occurrence data.
enumeration

Enumerations.
downloads

Downloads interface
occ_issues

Parse and examine further GBIF issues on a dataset.
suggestfields

Fields available in gbif_suggest function
stylegeojson

Style a data.frame prior to converting to geojson.
occ_download_import

Import a downloaded file from GBIF.
organizations

Organizations metadata.
name_backbone

Lookup names in the GBIF backbone taxonomy.
taxonsearch

Search for taxa in GBIF.
taxrank

Get the possible values to be used for (taxonomic) rank arguments in GBIF API methods.
occ_download_meta

Retrieves the occurrence download metadata by its unique key.
parsenames

Parse taxon names using the GBIF name parser.
providers

Get data providers and their unique keys.
occurrencelist_all

Occurrencelist_all carries out an occurrencelist query for a single name and all its name variants according to GBIF's name matching.
occurrencedensity

Returns summary counts of occurrence records by one-degree cell for a single taxon, country, dataset, data publisher or data network.
rgb_country_codes

Look up 2 character ISO country codes
occurrencelist

Occurrencelist searches for taxon concept records matching a range of filters.
occurrencelist_many

occurrencelist_many is the same as occurrencelist, but takes in a vector of species names.
togeojson

Convert spatial data files to GeoJSON from various formats.
rgbif-package

Interface to the Global Biodiversity Information Facility API.
resources

Get data resources and their unique keys.
rgbif-defunct

Defunct functions in rgbif
typestatus

Type status options for GBIF searching
taxonget

Get taxonomic information on a specific taxon or taxa in GBIF by their taxon concept keys.
taxoncount

Search by taxon to retrieve number of records in GBIF.
type_sum

Type summary
read_wkt

Check input WKT
occ_issues_lookup

Lookup occurrence issue definitions and short codes
occurrenceget

Get individual records for a given occurrence record.