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rgbif (version 0.8.0)

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

0.8.0

License

MIT + file LICENSE

Issues

37

Pull Requests

1

Stars

163

Forks

51

Maintainer

Scott Chamberlain

Last Published

March 9th, 2015

Functions in rgbif (0.8.0)

density_spplist

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

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

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

View highlighted terms in name results from 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.
gbif_bbox2wkt

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

Get Github credentials from use in console
gbifparser_verbatim

Parser for gbif data
namelkupparser

Parser for name_usage endpoints, for fxns name_lookup and name_backbone
gbif_capwords

Capitalize the first letter of a character string.
gbifmap_dens

Make a simple map to visualize GBIF data density data
networks

Networks metadata.
blanktheme

Custom ggplot2 theme
gist

Post a file as a Github gist
nodes

Nodes metadata.
count_facet

Facetted count occurrence search.
create_gist

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

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

Vector of fields in the output for the function occ_search
check_wkt

Check input WKT
gbifmap

Make a map to visualize GBIF occurrence data.
gbif_photos

View photos from GBIF.
gbifmap_list

Make a simple map to visualize GBIF point data.
gbifdata

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

Convert commas to periods in lat/long data
densitylist

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

Installations metadata.
elevation

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

Parse and examine further GBIF issues on a dataset.
ldfast

Replacement function for ldply that should be faster.
dataset_search

Search datasets in GBIF.
gbifparser

Parser for gbif data
datasets

Search for datasets and dataset metadata.
dataset_metrics

Get details on a GBIF dataset.
dataset_suggest

Suggest datasets in GBIF.
occ_get

Get data for specific GBIF occurrences.
parsenames

Parse taxon names using the GBIF name parser.
occurrencelist_all

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

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

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

Convert spatial data files to GeoJSON from various formats.
resources

Get data resources and their unique keys.
stylegeojson

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

Search by taxon to retrieve number of records in GBIF.
%>%

Pipe operator
providers

Get data providers and their unique keys.
taxonsearch

Search for taxa in GBIF.
taxrank

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

Type status options for GBIF searching
type_sum

Type summary
occurrencecount

Counts taxon concept records matching a range of filters.
rgbif-package

Interface to the Global Biodiversity Information Facility API.
occurrencedensity

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

Parse results from call to occurrencelist endpoint
name_backbone

Lookup names in the GBIF backbone taxonomy.
occurrenceget

Get individual records for a given occurrence record.
occurrencelist

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

Get number of occurrence records.
occ_issues_lookup

Lookup occurrence issue definitions and short codes
organizations

Organizations metadata.
occ_search

Search for GBIF occurrences.
rgbif-defunct

Defunct functions in rgbif
suggestfields

Fields available in gbif_suggest function
datasetparser

Parser for gbif data
rgb_country_codes

Look up 2 character ISO country codes
name_lookup

Lookup names in all taxonomies in GBIF.
taxonget

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