Learn R Programming
⚠️There's a newer version (3.8.1) of this package.Take me there.

rgbif (version 0.8.4)

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.

Copy Link

Version

Install

install.packages('rgbif')

Monthly Downloads

7,274

Version

0.8.4

License

MIT + file LICENSE

Issues

37

Pull Requests

1

Stars

163

Forks

51

Maintainer

Scott Chamberlain

Last Published

June 8th, 2015

Functions in rgbif (0.8.4)

gbif_capwords

Capitalize the first letter of a character string.
dataset_metrics

Get details on a GBIF dataset.
gbif_names

View highlighted terms in name results from GBIF.
create_gist

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

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

Parser for name_usage endpoints, for fxns name_lookup and name_backbone
name_lookup

Lookup names in all taxonomies in GBIF.
occ_issues_lookup

Lookup occurrence issue definitions and short codes
occ_count

Get number of occurrence records.
occ_issues

Parse and examine further GBIF issues on a dataset.
gbif_photos

View photos from GBIF.
occ_get

Get data for specific GBIF occurrences.
read_wkt

Check input WKT
densitylist

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

Parse taxon names using the GBIF name parser.
commas_to_periods

Convert commas to periods in lat/long data
blanktheme

Custom ggplot2 theme
gbifmap_list

Make a simple map to visualize GBIF point data.
organizations

Organizations metadata.
dataset_search

Search datasets 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.
gbifparser_verbatim

Parser for gbif data
occurrencecount

Counts taxon concept records matching a range of filters.
count_facet

Facetted count occurrence search.
gbifdata

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

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

Networks metadata.
nodes

Nodes metadata.
gist

Post a file as a Github gist
gbifmap_dens

Make a simple map to visualize GBIF data density data
occ_fields

Vector of fields in the output for the function occ_search
gbifparser

Parser for gbif data
check_wkt

Check input WKT
occurrencelist_many

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

Get Github credentials from use in console
occ_search

Search for GBIF occurrences.
providers

Get data providers and their unique keys.
isocodes

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

Search for datasets and dataset metadata.
occurrencelist_all

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

Suggest datasets in GBIF.
datasetparser

Parser for gbif data
gbif_bbox2wkt

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

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

Installations metadata.
occurrenceget

Get individual records for a given occurrence record.
gbifmap

Make a map to visualize GBIF occurrence data.
taxrank

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

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

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

Type summary
resources

Get data resources and their unique keys.
togeojson

Convert spatial data files to GeoJSON from various formats.
taxonsearch

Search for taxa in GBIF.
typestatus

Type status options for GBIF searching
taxonget

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

Interface to the Global Biodiversity Information Facility API.
parseresults

Parse results from call to occurrencelist endpoint
%>%

Pipe operator
taxoncount

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

Fields available in gbif_suggest function
rgb_country_codes

Look up 2 character ISO country codes
rgbif-defunct

Defunct functions in rgbif
enumeration

Enumerations.
elevation

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

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

Lookup names in the GBIF backbone taxonomy.