rgbif gives you access to data from GBIF via their REST API. GBIF versions their API - we are currently using v1 of their API. You can no longer use their old API in this package - see ?rgbif-defunct.
To get started, see:
- rgbif vignette (https://docs.ropensci.org/rgbif/articles/rgbif.html): an introduction to the package’s main functionalities.
- Function reference (https://docs.ropensci.org/rgbif/reference/index.html): an overview of all
rgbiffunctions. - Articles (https://docs.ropensci.org/rgbif/articles/index.html): vignettes/tutorials on how to download data, clean data, and work with taxonomic names.
- Occurrence manual (https://books.ropensci.org/occurrences/): a book covering a suite of R packages used for working with biological occurrence data.
Check out the rgbif paper for more information on this package and the sister Python and Ruby clients.
Package API
The rgbif package API follows the GBIF API, which has the following sections:
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registry(https://www.gbif.org/developer/registry) - Metadata on datasets, and contributing organizations, installations, networks, and nodes-
rgbiffunctions:dataset_metrics(),dataset_search(),dataset_suggest(),datasets(),enumeration(),enumeration_country(),installations(),networks(),nodes(),organizations() - Registry also includes the GBIF OAI-PMH service, which includes GBIF registry data only.
rgbiffunctions:gbif_oai_get_records(),gbif_oai_identify(),gbif_oai_list_identifiers(),gbif_oai_list_metadataformats(),gbif_oai_list_records(),gbif_oai_list_sets()
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species(https://www.gbif.org/developer/species) - Species names and metadata-
rgbiffunctions:name_backbone(),name_lookup(),name_suggest(),name_usage()
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occurrences(https://www.gbif.org/developer/occurrence) - Occurrences, both for the search and download APIs-
rgbiffunctions:occ_count(),occ_data(),occ_download(),occ_download_prep(),occ_download_queue(),occ_download_cancel(),occ_download_cancel_staged(),occ_download_get(),occ_download_import(),occ_download_list(),occ_download_meta(),occ_download_datasets(),occ_download_dataset_activity(),occ_get(),occ_issues(),occ_issues_lookup(),occ_metadata(),occ_search(),pred(),preds(),pred_multi()
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maps(https://www.gbif.org/developer/maps) - Map API-
rgbiffunctions:map_fetch() - Note: we used to have a function
gbifmap()that usedggplot2to plot data from the occurrence API, but it’s been removed - see package mapr
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Installation
install.packages("rgbif")
Or, install development version
install.packages("remotes") remotes::install_github("ropensci/rgbif")
library("rgbif")
Note: Windows users have to first install Rtools (https://cran.r-project.org/bin/windows/Rtools/) to use devtools
Mac Users: (in case of errors)
Terminal:
Install gdal : https://github.com/edzer/sfr/blob/master/README.md#macos
brew install opensslin R:
install.packages('openssl') install.packages('rgeos') install.packages('rgbif')
Search for occurrence data
occ_search(scientificName = "Ursus americanus", limit = 50) #> Records found [15107] #> Records returned [50] #> No. unique hierarchies [1] #> No. media records [50] #> No. facets [0] #> Args [limit=50, offset=0, scientificName=Ursus americanus, fields=all] #> # A tibble: 50 x 74 #> key scientificName decimalLatitude decimalLongitude issues datasetKey #> <chr> <chr> <dbl> <dbl> <chr> <chr> #> 1 2543… Ursus america… 42.5 -73.2 cdrou… 50c9509d-… #> 2 2550… Ursus america… 35.7 -83.5 cdrou… 50c9509d-… #> 3 2550… Ursus america… 31.3 -110. cdrou… 50c9509d-… #> 4 2550… Ursus america… 35.1 -118. cdrou… 50c9509d-… #> 5 2550… Ursus america… 25.2 -101. cdrou… 50c9509d-… #> 6 2550… Ursus america… 39.4 -120. cdrou… 50c9509d-… #> 7 2557… Ursus america… 43.8 -72.6 gass84 50c9509d-… #> 8 2557… Ursus america… 34.0 -92.6 cdrou… 50c9509d-… #> 9 2557… Ursus america… 34.0 -92.6 cdrou… 50c9509d-… #> 10 2557… Ursus america… 34.0 -92.6 cdrou… 50c9509d-… #> # … with 40 more rows, and 68 more variables: publishingOrgKey <chr>, #> # installationKey <chr>, publishingCountry <chr>, protocol <chr>, #> # lastCrawled <chr>, lastParsed <chr>, crawlId <int>, extensions <chr>, #> # basisOfRecord <chr>, taxonKey <int>, kingdomKey <int>, phylumKey <int>, #> # classKey <int>, orderKey <int>, familyKey <int>, genusKey <int>, #> # speciesKey <int>, acceptedTaxonKey <int>, acceptedScientificName <chr>, #> # kingdom <chr>, phylum <chr>, order <chr>, family <chr>, genus <chr>, #> # species <chr>, genericName <chr>, specificEpithet <chr>, taxonRank <chr>, #> # taxonomicStatus <chr>, dateIdentified <chr>, #> # coordinateUncertaintyInMeters <dbl>, stateProvince <chr>, year <int>, #> # month <int>, day <int>, eventDate <chr>, modified <chr>, #> # lastInterpreted <chr>, references <chr>, license <chr>, identifiers <chr>, #> # facts <chr>, relations <chr>, geodeticDatum <chr>, class <chr>, #> # countryCode <chr>, country <chr>, rightsHolder <chr>, identifier <chr>, #> # http...unknown.org.nick <chr>, verbatimEventDate <chr>, datasetName <chr>, #> # collectionCode <chr>, gbifID <chr>, verbatimLocality <chr>, #> # occurrenceID <chr>, taxonID <chr>, catalogNumber <chr>, recordedBy <chr>, #> # http...unknown.org.occurrenceDetails <chr>, institutionCode <chr>, #> # rights <chr>, eventTime <chr>, identificationID <chr>, name <chr>, #> # informationWithheld <chr>, occurrenceRemarks <chr>, #> # infraspecificEpithet <chr>
Or you can get the taxon key first with name_backbone(). Here, we select to only return the occurrence data.
key <- name_backbone(name='Helianthus annuus', kingdom='plants')$speciesKey occ_search(taxonKey=key, limit=20) #> Records found [44669] #> Records returned [20] #> No. unique hierarchies [1] #> No. media records [20] #> No. facets [0] #> Args [limit=20, offset=0, taxonKey=9206251, fields=all] #> # A tibble: 20 x 88 #> key scientificName decimalLatitude decimalLongitude issues datasetKey #> <chr> <chr> <dbl> <dbl> <chr> <chr> #> 1 2542… Helianthus an… 25.8 -100. cdrou… 50c9509d-… #> 2 2550… Helianthus an… 25.6 -100. cdrou… 50c9509d-… #> 3 2550… Helianthus an… 25.8 -101. cdrou… 50c9509d-… #> 4 2557… Helianthus an… 18.6 -99.2 cdrou… 50c9509d-… #> 5 2557… Helianthus an… 26.9 -101. cdrou… 50c9509d-… #> 6 2558… Helianthus an… 59.8 17.6 cdrou… 38b4c89f-… #> 7 2561… Helianthus an… 59.8 17.6 cdrou… 38b4c89f-… #> 8 2563… Helianthus an… 33.6 -112. cdrou… 50c9509d-… #> 9 2564… Helianthus an… 59.6 17.4 gass84 38b4c89f-… #> 10 2572… Helianthus an… 56.2 12.6 gass84 38b4c89f-… #> 11 2572… Helianthus an… 59.8 17.6 gass84 38b4c89f-… #> 12 2573… Helianthus an… 33.2 -112. cdrou… 50c9509d-… #> 13 2573… Helianthus an… 26.3 -98.2 cdrou… 50c9509d-… #> 14 2573… Helianthus an… 21.9 -102. cdrou… 50c9509d-… #> 15 2574… Helianthus an… 30.3 -97.7 cdrou… 50c9509d-… #> 16 1986… Helianthus an… 33.8 -118. cdrou… 50c9509d-… #> 17 1986… Helianthus an… 27.7 -97.3 cdrou… 50c9509d-… #> 18 1990… Helianthus an… 26.2 -98.2 cdrou… 50c9509d-… #> 19 1990… Helianthus an… 52.6 10.1 cdrou… 6ac3f774-… #> 20 1990… Helianthus an… 53.9 10.9 cdrou… 6ac3f774-… #> # … with 82 more variables: publishingOrgKey <chr>, installationKey <chr>, #> # publishingCountry <chr>, protocol <chr>, lastCrawled <chr>, #> # lastParsed <chr>, crawlId <int>, extensions <chr>, basisOfRecord <chr>, #> # taxonKey <int>, kingdomKey <int>, phylumKey <int>, classKey <int>, #> # orderKey <int>, familyKey <int>, genusKey <int>, speciesKey <int>, #> # acceptedTaxonKey <int>, acceptedScientificName <chr>, kingdom <chr>, #> # phylum <chr>, order <chr>, family <chr>, genus <chr>, species <chr>, #> # genericName <chr>, specificEpithet <chr>, taxonRank <chr>, #> # taxonomicStatus <chr>, dateIdentified <chr>, stateProvince <chr>, #> # year <int>, month <int>, day <int>, eventDate <chr>, modified <chr>, #> # lastInterpreted <chr>, references <chr>, license <chr>, identifiers <chr>, #> # facts <chr>, relations <chr>, geodeticDatum <chr>, class <chr>, #> # countryCode <chr>, country <chr>, rightsHolder <chr>, identifier <chr>, #> # http...unknown.org.nick <chr>, verbatimEventDate <chr>, datasetName <chr>, #> # collectionCode <chr>, gbifID <chr>, verbatimLocality <chr>, #> # occurrenceID <chr>, taxonID <chr>, catalogNumber <chr>, recordedBy <chr>, #> # http...unknown.org.occurrenceDetails <chr>, institutionCode <chr>, #> # rights <chr>, eventTime <chr>, identificationID <chr>, name <chr>, #> # coordinateUncertaintyInMeters <dbl>, continent <chr>, municipality <chr>, #> # county <chr>, identificationVerificationStatus <chr>, language <chr>, #> # type <chr>, occurrenceStatus <chr>, vernacularName <chr>, #> # taxonConceptID <chr>, informationWithheld <chr>, endDayOfYear <chr>, #> # locality <chr>, startDayOfYear <chr>, datasetID <chr>, accessRights <chr>, #> # higherClassification <chr>, occurrenceRemarks <chr>
Search for many species
Get the keys first with name_backbone(), then pass to occ_search()
splist <- c('Accipiter erythronemius', 'Junco hyemalis', 'Aix sponsa') keys <- sapply(splist, function(x) name_backbone(name=x)$speciesKey, USE.NAMES=FALSE) occ_search(taxonKey=keys, limit=5, hasCoordinate=TRUE) #> Records found [2480598 (35), 9362842 (5530216), 2498387 (1828163)] #> Records returned [2480598 (5), 9362842 (5), 2498387 (5)] #> No. unique hierarchies [2480598 (1), 9362842 (1), 2498387 (1)] #> No. media records [2480598 (5), 9362842 (5), 2498387 (5)] #> No. facets [2480598 (0), 9362842 (0), 2498387 (0)] #> Args [hasCoordinate=TRUE, limit=5, offset=0, taxonKey=2480598,9362842,2498387, #> fields=all] #> 3 requests; First 10 rows of data from 2480598 #> #> # A tibble: 5 x 67 #> key scientificName decimalLatitude decimalLongitude issues datasetKey #> <chr> <chr> <dbl> <dbl> <chr> <chr> #> 1 2243… Accipiter ery… -38.3 -60.4 "" b1047888-… #> 2 2432… Accipiter ery… -24.0 -52.2 "" b1047888-… #> 3 2243… Accipiter ery… -24.3 -48.4 "" b1047888-… #> 4 2243… Accipiter ery… -26.3 -48.6 "" b1047888-… #> 5 2243… Accipiter ery… -26.3 -48.6 "" b1047888-… #> # … with 61 more variables: publishingOrgKey <chr>, installationKey <chr>, #> # publishingCountry <chr>, protocol <chr>, lastCrawled <chr>, #> # lastParsed <chr>, crawlId <int>, extensions <chr>, basisOfRecord <chr>, #> # taxonKey <int>, kingdomKey <int>, phylumKey <int>, classKey <int>, #> # orderKey <int>, familyKey <int>, genusKey <int>, speciesKey <int>, #> # acceptedTaxonKey <int>, acceptedScientificName <chr>, kingdom <chr>, #> # phylum <chr>, order <chr>, family <chr>, genus <chr>, species <chr>, #> # genericName <chr>, specificEpithet <chr>, taxonRank <chr>, #> # taxonomicStatus <chr>, year <int>, month <int>, day <int>, eventDate <chr>, #> # lastInterpreted <chr>, references <chr>, license <chr>, identifiers <chr>, #> # facts <chr>, relations <chr>, geodeticDatum <chr>, class <chr>, #> # countryCode <chr>, country <chr>, rightsHolder <chr>, identifier <chr>, #> # verbatimEventDate <chr>, nomenclaturalCode <chr>, locality <chr>, #> # collectionCode <chr>, gbifID <chr>, occurrenceID <chr>, #> # catalogNumber <chr>, recordedBy <chr>, vernacularName <chr>, #> # fieldNotes <chr>, eventTime <chr>, behavior <chr>, verbatimElevation <chr>, #> # higherClassification <chr>, name <chr>, associatedTaxa <chr>
Maps
We’ve removed gbifmap() which helped users plot data from functions occ_search()/occ_data() - instead we strongly recommend using our other package mapr.
As of rgibf v1, we have integration for GBIF’s mapping API, which lets you get raster images of occurrences of taxa of interest. For example:
x <- map_fetch(taxonKey = 3118771, year = 2010) x #> class : RasterLayer #> dimensions : 512, 512, 262144 (nrow, ncol, ncell) #> resolution : 0.703125, 0.3515625 (x, y) #> extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) #> crs : +init=epsg:4326 +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 #> source : memory #> names : layer #> values : 0, 1 (min, max)
Contributors
Collected via GitHub Issues, this list honors all contributors in alphabetical order. Code contributors are in bold.
adamdsmith - AgustinCamacho - AldoCompagnoni - AlexPeap - andzandz11 - AshleyWoods - AugustT - barthoekstra - benmarwick - cathynewman - cboettig - coyotree - damianooldoni - dandaman - djokester - dlebauer - dmcglinn - dnoesgaard - DupontCai - ecology-data-science - EDiLD - elgabbas - emhart - fxi - ghost - gkburada - hadley - Huasheng12306 - ibartomeus - JanLauGe - jarioksa - jeroen - jhnwllr - jhpoelen - jivelasquezt - jkmccarthy - johnbaums - jtgiermakowski - jwhalennds - karthik - kgturner - Kim1801 - ljuliusson - ljvillanueva - luisDVA - martinpfannkuchen - MattBlissett - MattOates - maxhenschell - mdsumner - no-la-ngo - Octoberweather - Pakillo - peterdesmet - PhillRob - poldham - qgroom - raymondben - rossmounce - sacrevert - sagitaninta - sckott - scottsfarley93 - simon-tarr - SriramRamesh - stevenpbachman - stevensotelo - stevenysw - TomaszSuchan - tphilippi - vandit15 - vervis - vijaybarve - willgearty - Xuletajr - yvanlebras - zixuan75
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
rgbifin R doingcitation(package = 'rgbif') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
This package is part of a richer suite called spocc - Species Occurrence Data, along with several other packages, that provide access to occurrence records from multiple databases.
