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rgbif (version 0.9.0)

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

7,274

Version

0.9.0

License

MIT + file LICENSE

Issues

37

Pull Requests

1

Stars

163

Forks

51

Maintainer

Scott Chamberlain

Last Published

November 25th, 2015

Functions in rgbif (0.9.0)

gbif_issues

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

Convert commas to periods in lat/long data
rgbif-package

Interface to the Global Biodiversity Information Facility API.
occ_fields

Vector of fields in the output for the function occ_search
datasets

Search for datasets and dataset metadata.
taxoncount

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

Capitalize the first letter of a character string.
gbifmap

Make a map to visualize GBIF occurrence data.
occ_search

Search for GBIF occurrences.
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.
get_credentials

Get Github credentials from use in console
dataset_search

Search datasets in GBIF.
isocodes

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

View highlighted terms in name results from GBIF.
occ_issues_lookup

Lookup occurrence issue definitions and short codes
%>%

Pipe operator
occ_download_meta

Retrieves the occurrence download metadata by its unique key.
occ_get

Get data for specific GBIF occurrences.
resources

Get data resources and their unique keys.
check_wkt

Check input WKT
occurrencecount

Counts taxon concept records matching a range of filters.
dataset_metrics

Get details on a GBIF dataset.
gbif_citation

Get citation for datasets used
occ_download_list

Lists the downloads created by a user.
networks

Networks metadata.
nodes

Nodes metadata.
taxonget

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

Type summary
occurrencedensity

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

Get individual records for a given occurrence record.
occ_download_get

Get a download from GBIF.
gbif_oai

GBIF registry data via OAI-PMH
organizations

Organizations metadata.
rgbif-defunct

Defunct functions in rgbif
namelkupparser

Parser for name_usage endpoints, for fxns name_lookup and name_backbone
providers

Get data providers and their unique keys.
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.
gbifparser

Parser for gbif data
rgb_country_codes

Look up 2 character ISO country codes
dataset_suggest

Suggest datasets in GBIF.
stylegeojson

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

Fields available in gbif_suggest function
typestatus

Type status options for GBIF searching
gbif_bbox2wkt

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

Parse results from call to occurrencelist endpoint
downloads

Downloads interface
installations

Installations metadata.
blanktheme

Custom ggplot2 theme
count_facet

Facetted count occurrence search.
create_gist

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

Parser for gbif data
gbifdata

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

Lookup names in the GBIF backbone taxonomy.
enumeration

Enumerations.
name_lookup

Lookup names in all taxonomies in GBIF.
elevation

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

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

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

Make a simple map to visualize GBIF data density data
density_spplist

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

View photos from GBIF.
gist

Post a file as a Github gist
gbifmap_list

Make a simple map to visualize GBIF point data.
gbifparser_verbatim

Parser for gbif data
occ_count

Get number of occurrence records.
taxrank

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

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

Import a downloaded file from GBIF.
parsenames

Parse taxon names using the GBIF name parser.
taxonsearch

Search for taxa in GBIF.
occ_download

Spin up a download request for GBIF occurrence data.
occ_issues

Parse and examine further GBIF issues on a dataset.
occurrencelist

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

Check input WKT
togeojson

Convert spatial data files to GeoJSON from various formats.