Package index • rgbif

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)

Occurrence search

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(): Lookup names in the GBIF backbone taxonomy.

name_backbone_checklist(): Lookup 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.

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)

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.