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rgbif

High level overview of package

rgbif-package rgbif
Interface to the Global Biodiversity Information Facility API.

Occurrence downloads

Work with the GBIF occurrence downloads APIs https://www.gbif.org/developer/occurrence#download

occ_download() occ_download_prep()
Spin up a download request for GBIF occurrence data.
occ_download_cached()
Check for downloads already in your GBIF account
occ_download_cancel() occ_download_cancel_staged()
Cancel a download creation process.
occ_download_dataset_activity()
Lists the downloads activity of a dataset
occ_download_datasets()
List datasets for a download
occ_download_describe()
Describes the fields available in GBIF downloads
occ_download_doi()
Get download meta data from a doi
occ_download_get()
Get a download from GBIF.
occ_download_import() as.download()
Import a downloaded file from GBIF.
occ_download_list()
Lists the downloads created by a user.
occ_download_meta()
Retrieves the occurrence download metadata by its unique key.
occ_download_queue()
Download requests in a queue
occ_download_sql() occ_download_sql_validate() occ_download_sql_prep()
Download occurrence data using a SQL query
occ_download_wait()
Wait for an occurrence download to be done
downloads
Downloads interface
pred() pred_gt() pred_gte() pred_lt() pred_lte() pred_not() pred_like() pred_within() pred_isnull() pred_notnull() pred_or() pred_and() pred_in() pred_default()
Download predicate DSL (domain specific language)

Work with the GBIF occurrence search APIs https://www.gbif.org/developer/occurrence

occ_get() occ_get_verbatim()
Get data for GBIF occurrences by occurrence key
occ_data()
Legacy alternative to occ_search
occ_metadata()
Search for catalog numbers, collection codes, collector names, and institution codes.
occ_search()
Search for GBIF occurrences
occ_count()
Get number of occurrence records.
occ_count_country() occ_count_pub_country() occ_count_year() occ_count_basis_of_record()
Get quick pre-computed occurrence counts of a limited number of dimensions.

Taxonomic names

Work with the GBIF taxonomic names API https://www.gbif.org/developer/species

name_backbone() name_backbone_verbose()
Match names to GBIF backbone and other checklists.
name_backbone_checklist()
Match names in the GBIF backbone taxonomy in a checklist.
name_issues()
Parse and examine further GBIF name issues on a dataset.
name_lookup()
Lookup names in all taxonomies in GBIF.
name_parse()
Parse taxon names using the GBIF name parser.
name_suggest()
Suggest up to 20 name usages.
name_usage()
Lookup details for specific names in all taxonomies in GBIF.

Citation

https://docs.ropensci.org/rgbif/articles/gbif_citations.html

gbif_citation()
Get citation for datasets used
derived_dataset() derived_dataset_prep()
Register a derived dataset for citation.

Geometry

check_wkt()
Check input WKT
gbif_bbox2wkt() gbif_wkt2bbox()
Convert a bounding box to a Well Known Text polygon, and a WKT to a bounding box
gbif_geocode()
Geocode lat-lon point(s) with GBIF's set of geo-polygons (experimental)

Registry

GBIF registry functions https://www.gbif.org/developer/registry

dataset_doi()
Get a GBIF dataset from a doi
dataset_gridded()
Check if a dataset is gridded
dataset_duplicate() dataset_noendpoint()
List datasets that are deleted or have no endpoint.
dataset_export() dataset_search() dataset_suggest()
Search for dataset metadata.
dataset_get() dataset_process() dataset_networks() dataset_constituents() dataset_comment() dataset_contact() dataset_endpoint() dataset_identifier() dataset_machinetag() dataset_tag() dataset_metrics()
Get dataset metadata using a datasetkey
dataset()
Search for more obscure dataset metadata.
organizations()
Organizations metadata.
network() network_constituents()
Get data about GBIF networks
nodes()
Nodes metadata.
installations()
Installations metadata.
installation_search()
Search for installations
installation_dataset() installation_comment() installation_contact() installation_endpoint() installation_identifier() installation_machinetag() installation_tag()
Get installation metadata using an installation key

OAI

gbif_oai_identify() gbif_oai_list_identifiers() gbif_oai_list_records() gbif_oai_list_metadataformats() gbif_oai_list_sets() gbif_oai_get_records()
GBIF registry data via OAI-PMH

Maps

Work with the GBIF Maps API https://www.gbif.org/developer/maps

map_fetch()
Fetch maps of GBIF occurrences
mvt_fetch()
Fetch Map Vector Tiles (MVT)

GRSciColl

institution_search() institution_export()
Search GRSciColl institutions
collection_search() collection_export()
Search GRSciColl collections

Miscellaneous

rgb_country_codes()
Look up 2 character ISO country codes
taxrank()
Get the possible values to be used for (taxonomic) rank arguments in GBIF API methods.
wkt_parse()
parse wkt into smaller bits
elevation()
Get elevation for lat/long points from a data.frame or list of points.
enumeration() enumeration_country()
Enumerations.
gbif_issues()
List all GBIF issues and their codes.
gbif_issues_lookup()
Lookup issue definitions and short codes
lit_search() lit_count() lit_export()
Search for literature that cites GBIF mediated data

Pretty html reports

gbif_names()
View highlighted terms in name results from GBIF.
gbif_photos()
View photos from GBIF.

Defunct functions

datasets()
Search for datasets and dataset metadata.
rgbif-defunct
Defunct functions in rgbif
parsenames()
Parse taxon names using the GBIF name parser.
networks()
Networks metadata.
count_facet()
Facetted count occurrence search.
occ_facet()
Facet GBIF occurrences
occ_issues()
Parse and examine further GBIF occurrence issues on a dataset.