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rgbif (version 0.9.3)

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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Install

install.packages('rgbif')

Monthly Downloads

9,086

Version

0.9.3

License

MIT + file LICENSE

Issues

36

Pull Requests

0

Stars

173

Forks

52

Maintainer

Scott Chamberlain

Last Published

March 29th, 2016

Functions in rgbif (0.9.3)

occ_download_meta

Retrieves the occurrence download metadata by its unique key.
blanktheme

Custom ggplot2 theme
create_gist

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

Import a downloaded file from GBIF.
gbifdata

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

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

GBIF registry data via OAI-PMH
check_wkt

Check input WKT
occurrencelist_many

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

View photos from GBIF.
name_lookup

Lookup names in all taxonomies in GBIF.
get_credentials

Get Github credentials from use in console
occ_download

Spin up a download request for GBIF occurrence data.
count_facet

Facetted count occurrence search.
elevation

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

Check input WKT
gist

Post a file as a Github gist
occ_download_cancel

Cancel a download cretion process.
densitylist

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

Search datasets in GBIF.
gbif_issues

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

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

Search for datasets and dataset metadata.
gbif_citation

Get citation for datasets used
occ_count

Get number of occurrence records.
occ_issues_lookup

Lookup occurrence issue definitions and short codes
nodes

Nodes metadata.
isocodes

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

Lookup names in the GBIF backbone taxonomy.
networks

Networks metadata.
dataset_suggest

Suggest datasets in GBIF.
installations

Installations metadata.
downloads

Downloads interface
dataset_metrics

Get details on a GBIF dataset.
occurrencedensity

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

Get data for specific GBIF occurrences.
density_spplist

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

Make a simple map to visualize GBIF point data.
occ_download_get

Get a download from GBIF.
parsenames

Parse taxon names using the GBIF name parser.
gbifmap_dens

Make a simple map to visualize GBIF data density data
occurrenceget

Get individual records for a given occurrence record.
gbif_bbox2wkt

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

Vector of fields in the output for the function occ_search
occ_data

Search for GBIF occurrences - simplified for speed
enumeration

Enumerations.
occ_issues

Parse and examine further GBIF issues on a dataset.
gbif_names

View highlighted terms in name results from GBIF.
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.
occurrencelist

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

Search for GBIF occurrences
%>%

Pipe operator
occ_download_list

Lists the downloads created by a user.
occurrencecount

Counts taxon concept records matching a range of filters.
gbifmap

Make a map to visualize GBIF occurrence data.
organizations

Organizations metadata.
resources

Get data resources and their unique keys.
stylegeojson

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

Search for taxa in GBIF.
rgb_country_codes

Look up 2 character ISO country codes
wkt_parse

parse wkt into smaller bits
typestatus

Type status options for GBIF searching
taxoncount

Search by taxon to retrieve number of records in GBIF.
rgbif-package

Interface to the Global Biodiversity Information Facility API.
taxonget

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

Fields available in gbif_suggest function
type_sum

Type summary
taxrank

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

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

Defunct functions in rgbif
providers

Get data providers and their unique keys.