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rgbif (version 0.8.9)

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

0.8.9

License

MIT + file LICENSE

Issues

36

Pull Requests

0

Stars

173

Forks

52

Maintainer

Scott Chamberlain

Last Published

October 7th, 2015

Functions in rgbif (0.8.9)

commas_to_periods

Convert commas to periods in lat/long data
occ_download_meta

Retrieves the occurrence download metadata by its unique key.
dataset_metrics

Get details on a GBIF dataset.
read_wkt

Check input WKT
gbif_photos

View photos from GBIF.
occ_download_import

Import a downloaded file from GBIF.
create_gist

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

Make a simple map to visualize GBIF data density data
taxoncount

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

Spin up a download request for GBIF occurrence data.
gbif_names

View highlighted terms in name results from GBIF.
nodes

Nodes metadata.
rgbif-package

Interface to the Global Biodiversity Information Facility API.
blanktheme

Custom ggplot2 theme
gbifdata

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

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

Lookup occurrence issue definitions and short codes
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_capwords

Capitalize the first letter of a character string.
typestatus

Type status options for GBIF searching
dataset_suggest

Suggest datasets in GBIF.
isocodes

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

Enumerations.
gbifparser

Parser for gbif data
parsenames

Parse taxon names using the GBIF name parser.
datasets

Search for datasets and dataset metadata.
occ_get

Get data for specific GBIF occurrences.
%>%

Pipe operator
densitylist

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

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

Make a map to visualize GBIF occurrence data.
providers

Get data providers and their unique keys.
namelkupparser

Parser for name_usage endpoints, for fxns name_lookup and name_backbone
stylegeojson

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

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

Search datasets in GBIF.
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
togeojson

Convert spatial data files to GeoJSON from various formats.
gist

Post a file as a Github gist
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_issues

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

Networks metadata.
occ_download_cancel

Cancel a download cretion process.
occ_issues

Parse and examine further GBIF issues on a dataset.
taxonsearch

Search for taxa in GBIF.
count_facet

Facetted count occurrence search.
datasetparser

Parser for gbif data
rgb_country_codes

Look up 2 character ISO country codes
occ_fields

Vector of fields in the output for the function occ_search
type_sum

Type summary
occurrencelist_many

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

Get data resources and their unique keys.
parseresults

Parse results from call to occurrencelist endpoint
organizations

Organizations metadata.
check_wkt

Check input WKT
occurrencelist

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

Parser for gbif data
suggestfields

Fields available in gbif_suggest function
get_credentials

Get Github credentials from use in console
rgbif-defunct

Defunct functions in rgbif
taxonget

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

Get number of occurrence records.
name_backbone

Lookup names in the GBIF backbone taxonomy.
installations

Installations metadata.
occ_search

Search for GBIF occurrences.
gbifmap_list

Make a simple map to visualize GBIF point data.
name_lookup

Lookup names in all taxonomies in GBIF.
downloads

Downloads interface
name_usage

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

Get a download from GBIF.
occurrencecount

Counts taxon concept records matching a range of filters.
occ_download_list

Lists the downloads created by a user.
occurrencedensity

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

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