Package: rgbif 3.8.1.1

John Waller

rgbif: Interface to the Global Biodiversity Information Facility API

A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/developer/summary>). 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, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.

Authors:Scott Chamberlain [aut], Damiano Oldoni [aut], Vijay Barve [ctb], Peter Desmet [ctb], Laurens Geffert [ctb], Dan Mcglinn [ctb], Karthik Ram [ctb], rOpenSci [fnd], John Waller [aut, cre]

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rgbif.pdf |rgbif.html✨
rgbif/json (API)
NEWS

# Install 'rgbif' in R:
install.packages('rgbif', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/rgbif/issues

On CRAN:

gbifspecimensapiweb-servicesoccurrencesspeciestaxonomybiodiversitydatalifewatchoscibiospocc

13.27 score 155 stars 19 packages 2.0k scripts 8.5k downloads 42 mentions 113 exports 49 dependencies

Last updated 1 months agofrom:467e5e1c13 (on master). Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-winOKNov 15 2024
R-4.5-linuxOKNov 15 2024
R-4.4-winOKNov 15 2024
R-4.4-macOKNov 15 2024
R-4.3-winOKNov 15 2024
R-4.3-macOKNov 15 2024

Exports:%>%as.downloadblankthemecheck_wktcount_facetdatasetdataset_commentdataset_constituentsdataset_contactdataset_doidataset_duplicatedataset_endpointdataset_exportdataset_getdataset_griddeddataset_identifierdataset_machinetagdataset_metricsdataset_networksdataset_noendpointdataset_processdataset_searchdataset_suggestdataset_tagdatasetsderived_datasetderived_dataset_prepDownReqelevationenumerationenumeration_countrygbif_bbox2wktgbif_citationgbif_geocodegbif_issuesgbif_issues_lookupgbif_namesgbif_oai_get_recordsgbif_oai_identifygbif_oai_list_identifiersgbif_oai_list_metadataformatsgbif_oai_list_recordsgbif_oai_list_setsgbif_photosgbif_wkt2bboxGbifQueueinstallationslit_countlit_searchmap_fetchmvt_fetchname_backbonename_backbone_checklistname_backbone_verbosename_issuesname_lookupname_parsename_suggestname_usagenetworknetwork_constituentsnetworksnodesocc_countocc_count_basis_of_recordocc_count_countryocc_count_pub_countryocc_count_yearocc_dataocc_downloadocc_download_cachedocc_download_cancelocc_download_cancel_stagedocc_download_dataset_activityocc_download_datasetsocc_download_describeocc_download_getocc_download_importocc_download_listocc_download_metaocc_download_prepocc_download_queueocc_download_sqlocc_download_sql_prepocc_download_sql_validateocc_download_waitocc_facetocc_getocc_get_verbatimocc_issuesocc_metadataocc_searchocc_spellcheckorganizationsparsenamespredpred_andpred_defaultpred_gtpred_gtepred_inpred_isnullpred_likepred_ltpred_ltepred_notpred_notnullpred_orpred_withinrgb_country_codessuggestfieldstaxrankwkt_parse

Dependencies:askpassclicolorspacecrulcurldata.tablefansifarverggplot2gluegtablehttpcodehttrisobandjsonlitelabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeoaiopensslpillarpkgconfigplyrR6RColorBrewerRcpprlangscalesstringistringrsystibbletriebeardurltoolsutf8vctrsviridisLitewhiskerwithrwkxml2

Readme and manuals

Help Manual

Help pageTopics
Interface to the Global Biodiversity Information Facility API.rgbif-package rgbif
Check input WKTcheck_wkt
Facetted count occurrence search.count_facet
Search for more obscure dataset metadata.dataset
Get a GBIF dataset from a doidataset_doi
Check if a dataset is griddeddataset_gridded
List datasets that are deleted or have no endpoint.dataset_duplicate dataset_list_funs dataset_noendpoint
Search for dataset metadata.dataset_export dataset_search dataset_suggest
Get dataset metadata using a datasetkeydataset_comment dataset_constituents dataset_contact dataset_endpoint dataset_get dataset_identifier dataset_machinetag dataset_metrics dataset_networks dataset_process dataset_tag dataset_uuid_funs
Search for datasets and dataset metadata.datasets
Register a derived dataset for citation.derived_dataset derived_dataset_prep
Download predicate DSL (domain specific language)download_predicate_dsl pred pred_and pred_default pred_gt pred_gte pred_in pred_isnull pred_like pred_lt pred_lte pred_not pred_notnull pred_or pred_within
Downloads interfacedownloads
Get elevation for lat/long points from a data.frame or list of points.elevation
Enumerations.enumeration enumeration_country
Convert a bounding box to a Well Known Text polygon, and a WKT to a bounding boxgbif_bbox2wkt gbif_wkt2bbox
Get citation for datasets usedgbif_citation
Geocode lat-lon point(s) with GBIF's set of geo-polygons (experimental)gbif_geocode
List all GBIF issues and their codes.gbif_issues
Lookup issue definitions and short codesgbif_issues_lookup
View highlighted terms in name results from GBIF.gbif_names
GBIF registry data via OAI-PMHgbif_oai gbif_oai_get_records gbif_oai_identify gbif_oai_list_identifiers gbif_oai_list_metadataformats gbif_oai_list_records gbif_oai_list_sets
View photos from GBIF.gbif_photos
Installations metadata.installations
Search for literature that cites GBIF mediated datalit_count lit_search
Fetch maps of GBIF occurrencesmap_fetch
Fetch Map Vector Tiles (MVT)mvt_fetch
Lookup names in the GBIF backbone taxonomy.name_backbone name_backbone_verbose
Lookup names in the GBIF backbone taxonomy in a checklist.name_backbone_checklist
Parse and examine further GBIF name issues on a dataset.name_issues
Lookup names in all taxonomies in GBIF.name_lookup
Parse taxon names using the GBIF name parser.name_parse
Suggest up to 20 name usages.name_suggest
Lookup details for specific names in all taxonomies in GBIF.name_usage
Get data about GBIF networksnetwork network_constituents
Networks metadata.networks
Nodes metadata.nodes
Get number of occurrence records.occ_count
Get quick pre-computed occurrence counts of a limited number of dimensions.occ_count_ occ_count_basis_of_record occ_count_country occ_count_pub_country occ_count_year
Legacy alternative to occ_searchocc_data
Spin up a download request for GBIF occurrence data.occ_download occ_download_prep
Check for downloads already in your GBIF accountocc_download_cached
Cancel a download creation process.occ_download_cancel occ_download_cancel_staged
Lists the downloads activity of a datasetocc_download_dataset_activity
List datasets for a downloadocc_download_datasets
Describes the fields available in GBIF downloadsocc_download_describe
Get a download from GBIF.occ_download_get
Import a downloaded file from GBIF.as.download as.download.character as.download.download occ_download_import
Lists the downloads created by a user.occ_download_list
Retrieves the occurrence download metadata by its unique key.occ_download_meta
Download requests in a queueocc_download_queue
Download occurrence data using a SQL queryocc_download_sql occ_download_sql_prep occ_download_sql_validate
Wait for an occurrence download to be doneocc_download_wait
Facet GBIF occurrencesocc_facet
Get data for GBIF occurrences by occurrence keyocc_get occ_get_verbatim
Parse and examine further GBIF occurrence issues on a dataset.occ_issues
Search for catalog numbers, collection codes, collector names, and institution codes.occ_metadata
Search for GBIF occurrencesocc_search
Organizations metadata.organizations
Parse taxon names using the GBIF name parser.parsenames
Look up 2 character ISO country codesrgb_country_codes
Defunct functions in rgbifrgbif-defunct
Get the possible values to be used for (taxonomic) rank arguments in GBIF API methods.taxrank
parse wkt into smaller bitswkt_parse