rgbif v0.9.2

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Interface to the Global 'Biodiversity' Information Facility 'API'

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.

Functions in rgbif

Name Description
%>% Pipe operator
occ_get Get data for specific GBIF occurrences.
gbif_photos View photos from GBIF.
occ_download_get Get a download from GBIF.
dataset_suggest Suggest datasets in GBIF.
dataset_metrics Get details on a GBIF dataset.
blanktheme Custom ggplot2 theme
densitylist The density web service provides access to records showing the density of occurrence records from the GBIF Network by one-degree cell.
density_spplist The density web service provides access to records showing the density of occurrence records from the GBIF Network by one-degree cell.
check_wkt Check input WKT
occ_count Get number of occurrence records.
create_gist Function that takes a list of files and creates payload for API
gbif_oai GBIF registry data via OAI-PMH
name_lookup Lookup names in all taxonomies in GBIF.
gbif_names View highlighted terms in name results from GBIF.
occ_download_list Lists the downloads created by a user.
isocodes Table of country two character ISO codes, and GBIF names
count_facet Facetted count occurrence search.
dataset_search Search datasets in GBIF.
datasets Search for datasets and dataset metadata.
gbif_bbox2wkt Convert a bounding box to a Well Known Text polygon, and a WKT to a bounding box
gbif_issues Table of GBIF issues, with codes used in data output, full issue name, and descriptions.
gbifdata Get data.frame from occurrencelist, occurrencelist_many, or densitylist.
elevation Get elevation for lat/long points from a data.frame or list of points.
installations Installations metadata.
occ_data Search for GBIF occurrences - simplified for speed
name_usage Lookup details for specific names in all taxonomies in GBIF.
gbif_citation Get citation for datasets used
nodes Nodes metadata.
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.
gist Post a file as a Github gist
networks Networks metadata.
occ_fields Vector of fields in the output for the function occ_search
occurrencecount Counts taxon concept records matching a range of filters.
gbifmap_dens Make a simple map to visualize GBIF data density data
gbifmap_list Make a simple map to visualize GBIF point data.
get_credentials Get Github credentials from use in console
gbifmap Make a map to visualize GBIF occurrence data.
occ_search Search for GBIF occurrences
occ_download_cancel Cancel a download cretion process.
occ_download Spin up a download request for GBIF occurrence data.
enumeration Enumerations.
downloads Downloads interface
occ_issues Parse and examine further GBIF issues on a dataset.
suggestfields Fields available in gbif_suggest function
stylegeojson Style a data.frame prior to converting to geojson.
occ_download_import Import a downloaded file from GBIF.
organizations Organizations metadata.
name_backbone Lookup names in the GBIF backbone taxonomy.
taxonsearch Search for taxa in GBIF.
taxrank Get the possible values to be used for (taxonomic) rank arguments in GBIF API methods.
occ_download_meta Retrieves the occurrence download metadata by its unique key.
parsenames Parse taxon names using the GBIF name parser.
providers Get data providers and their unique 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.
occurrencedensity Returns summary counts of occurrence records by one-degree cell for a single taxon, country, dataset, data publisher or data network.
rgb_country_codes Look up 2 character ISO country codes
occurrencelist Occurrencelist searches for taxon concept records matching a range of filters.
occurrencelist_many occurrencelist_many is the same as occurrencelist, but takes in a vector of species names.
togeojson Convert spatial data files to GeoJSON from various formats.
rgbif-package Interface to the Global Biodiversity Information Facility API.
resources Get data resources and their unique keys.
rgbif-defunct Defunct functions in rgbif
typestatus Type status options for GBIF searching
taxonget Get taxonomic information on a specific taxon or taxa in GBIF by their taxon concept keys.
taxoncount Search by taxon to retrieve number of records in GBIF.
type_sum Type summary
read_wkt Check input WKT
occ_issues_lookup Lookup occurrence issue definitions and short codes
occurrenceget Get individual records for a given occurrence record.
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License MIT + file LICENSE
URL https://github.com/ropensci/rgbif
BugReports https://github.com/ropensci/rgbif/issues
LazyData true
VignetteBuilder knitr
RoxygenNote 5.0.1
NeedsCompilation no
Packaged 2016-02-02 01:30:01 UTC; sacmac
Repository CRAN
Date/Publication 2016-02-02 12:22:49

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