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rgbif's Introduction

rgbif

Project Status: Active – The project has reached a stable, usable state and is being actively developed. cran checks Build Status codecov.io rstudio mirror downloads cran version DOI

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.

Tutorials:

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:

  • registry (https://www.gbif.org/developer/registry) - Metadata on datasets, and contributing organizations, installations, networks, and nodes
    • rgbif functions: 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. rgbif functions: gbif_oai_get_records(), gbif_oai_identify(), gbif_oai_list_identifiers(), gbif_oai_list_metadataformats(), gbif_oai_list_records(), gbif_oai_list_sets()
  • species (https://www.gbif.org/developer/species) - Species names and metadata
    • rgbif functions: name_backbone(), name_lookup(), name_suggest(), name_usage()
  • occurrences (https://www.gbif.org/developer/occurrence) - Occurrences, both for the search and download APIs
    • rgbif functions: 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()
  • maps (https://www.gbif.org/developer/maps) - Map API
    • rgbif functions: map_fetch()
    • Note: we used to have a function gbifmap() that used ggplot2 to plot data from the occurrence API, but it's been removed - see package mapr

Installation

install.packages("rgbif")

Alternatively, install development version

install.packages("devtools")
devtools::install_github("ropensci/rgbif")
library("rgbif")

Note: Windows users have to first install 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 openssl

R terminal:

install.packages('openssl')
install.packages('rgeos')
install.packages('rgbif')

Search for occurrence data

occ_search(scientificName = "Ursus americanus", limit = 50)
#> Records found [10689] 
#> Records returned [50] 
#> No. unique hierarchies [1] 
#> No. media records [49] 
#> No. facets [0] 
#> Args [limit=50, offset=0, scientificName=Ursus americanus, fields=all] 
#> # A tibble: 50 x 69
#>    name        key decimalLatitude decimalLongitude issues  datasetKey    
#>    <chr>     <int>           <dbl>            <dbl> <chr>   <chr>         
#>  1 Ursus …  1.84e9            49.4           -123.  cdroun… 50c9509d-22c7…
#>  2 Ursus …  1.81e9            37.7           -120.  cdroun… 50c9509d-22c7…
#>  3 Ursus …  1.80e9            30.0            -84.3 cdroun… 50c9509d-22c7…
#>  4 Ursus …  1.81e9            42.0           -124.  cdroun… 50c9509d-22c7…
#>  5 Ursus …  1.81e9            25.4           -101.  gass84  50c9509d-22c7…
#>  6 Ursus …  1.81e9            40.8            -81.7 cdroun… 50c9509d-22c7…
#>  7 Ursus …  1.80e9            29.3           -103.  cdroun… 50c9509d-22c7…
#>  8 Ursus …  1.81e9            34.4           -119.  gass84  50c9509d-22c7…
#>  9 Ursus …  1.84e9            44.9           -110.  cdroun… 50c9509d-22c7…
#> 10 Ursus …  1.84e9            34.0           -117.  gass84  50c9509d-22c7…
#> # ... with 40 more rows, and 63 more variables: publishingOrgKey <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>, scientificName <chr>, kingdom <chr>,
#> #   phylum <chr>, order <chr>, family <chr>, genus <chr>, species <chr>,
#> #   genericName <chr>, specificEpithet <chr>, taxonRank <chr>,
#> #   dateIdentified <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>,
#> #   verbatimEventDate <chr>, datasetName <chr>, collectionCode <chr>,
#> #   gbifID <chr>, verbatimLocality <chr>, occurrenceID <chr>,
#> #   taxonID <chr>, recordedBy <chr>, catalogNumber <chr>,
#> #   http...unknown.org.occurrenceDetails <chr>, institutionCode <chr>,
#> #   rights <chr>, eventTime <chr>, occurrenceRemarks <chr>,
#> #   http...unknown.org.http_..rs.gbif.org.terms.1.0.Multimedia <chr>,
#> #   identificationID <chr>, infraspecificEpithet <chr>,
#> #   coordinateUncertaintyInMeters <dbl>, informationWithheld <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 [41219] 
#> Records returned [20] 
#> No. unique hierarchies [1] 
#> No. media records [15] 
#> No. facets [0] 
#> Args [limit=20, offset=0, taxonKey=9206251, fields=all] 
#> # A tibble: 20 x 91
#>    name        key decimalLatitude decimalLongitude issues   datasetKey   
#>    <chr>     <int>           <dbl>            <dbl> <chr>    <chr>        
#>  1 Helian…  1.81e9            52.6             10.1 cdround… 6ac3f774-d9f…
#>  2 Helian…  1.84e9             0                0   cucdmis… d2470ef8-edf…
#>  3 Helian…  1.81e9            32.0           -102.  cdround… 50c9509d-22c…
#>  4 Helian…  1.84e9            33.9           -117.  cdround… 50c9509d-22c…
#>  5 Helian…  1.82e9            56.6             16.4 cdround… 38b4c89f-584…
#>  6 Helian…  1.84e9            34.1           -116.  gass84   50c9509d-22c…
#>  7 Helian…  1.81e9            25.7           -100.  cdround… 50c9509d-22c…
#>  8 Helian…  1.82e9            56.6             16.6 cdround… 38b4c89f-584…
#>  9 Helian…  1.81e9            25.6           -100.  cdround… 50c9509d-22c…
#> 10 Helian…  1.82e9            59.8             17.5 gass84,… 38b4c89f-584…
#> 11 Helian…  1.83e9            34.0           -117.  cdround… 50c9509d-22c…
#> 12 Helian…  1.83e9            58.6             16.2 gass84,… 38b4c89f-584…
#> 13 Helian…  1.83e9            58.4             14.9 gass84,… 38b4c89f-584…
#> 14 Helian…  1.81e9            25.7           -100.  cdround… 50c9509d-22c…
#> 15 Helian…  1.84e9            26.2            -98.3 cdround… 50c9509d-22c…
#> 16 Helian…  1.84e9            25.8           -100.  cdround… 50c9509d-22c…
#> 17 Helian…  1.85e9            23.7            -99.2 cdround… 50c9509d-22c…
#> 18 Helian…  1.84e9           -43.6            173.  cdround… 50c9509d-22c…
#> 19 Helian…  1.84e9            23.8           -107.  cdround… 50c9509d-22c…
#> 20 Helian…  1.84e9            23.9           -107.  cdround… 50c9509d-22c…
#> # ... with 85 more variables: publishingOrgKey <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>, scientificName <chr>, kingdom <chr>,
#> #   phylum <chr>, order <chr>, family <chr>, genus <chr>, species <chr>,
#> #   genericName <chr>, specificEpithet <chr>, taxonRank <chr>,
#> #   coordinateUncertaintyInMeters <dbl>, year <int>, month <int>,
#> #   day <int>, eventDate <chr>, lastInterpreted <chr>, license <chr>,
#> #   identifiers <chr>, facts <chr>, relations <chr>, geodeticDatum <chr>,
#> #   class <chr>, countryCode <chr>, country <chr>, recordedBy <chr>,
#> #   catalogNumber <chr>, institutionCode <chr>, locality <chr>,
#> #   collectionCode <chr>, gbifID <chr>,
#> #   http...unknown.org.http_..rs.gbif.org.terms.1.0.Multimedia <chr>,
#> #   elevation <dbl>, elevationAccuracy <dbl>, continent <chr>,
#> #   stateProvince <chr>, rightsHolder <chr>, recordNumber <chr>,
#> #   identifier <chr>, municipality <chr>, datasetName <chr>,
#> #   language <chr>, occurrenceID <chr>, type <chr>,
#> #   ownerInstitutionCode <chr>, occurrenceRemarks <chr>,
#> #   dateIdentified <chr>, modified <chr>, references <chr>,
#> #   verbatimEventDate <chr>, verbatimLocality <chr>, taxonID <chr>,
#> #   http...unknown.org.occurrenceDetails <chr>, rights <chr>,
#> #   eventTime <chr>, identificationID <chr>, individualCount <int>,
#> #   county <chr>, identificationVerificationStatus <chr>,
#> #   occurrenceStatus <chr>, vernacularName <chr>, taxonConceptID <chr>,
#> #   informationWithheld <chr>, endDayOfYear <chr>, startDayOfYear <chr>,
#> #   datasetID <chr>, accessRights <chr>, higherClassification <chr>,
#> #   habitat <chr>, identifiedBy <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)
#> Occ. found [2480598 (16), 9362842 (3800072), 2498387 (1243725)] 
#> Occ. returned [2480598 (5), 9362842 (5), 2498387 (5)] 
#> No. unique hierarchies [2480598 (1), 9362842 (1), 2498387 (1)] 
#> No. media records [2480598 (1), 9362842 (5), 2498387 (3)] 
#> 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 81
#>   name         key decimalLatitude decimalLongitude issues   datasetKey   
#>   <chr>      <int>           <dbl>            <dbl> <chr>    <chr>        
#> 1 Accipit…  1.00e9          -27.6             -58.7 bri,cud… ad43e954-dd7…
#> 2 Accipit…  1.00e9          -27.9             -59.1 bri,cud… ad43e954-dd7…
#> 3 Accipit…  6.86e8            5.27            -60.7 cdround  e635240a-3cb…
#> 4 Accipit…  1.00e9          -27.6             -58.7 bri,cud… ad43e954-dd7…
#> 5 Accipit…  1.00e9          -27.6             -58.7 bri,cud… ad43e954-dd7…
#> # ... with 75 more variables: publishingOrgKey <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>, scientificName <chr>, kingdom <chr>,
#> #   phylum <chr>, order <chr>, family <chr>, genus <chr>, species <chr>,
#> #   genericName <chr>, specificEpithet <chr>, taxonRank <chr>, year <int>,
#> #   month <int>, day <int>, eventDate <chr>, modified <chr>,
#> #   lastInterpreted <chr>, license <chr>, identifiers <chr>, facts <chr>,
#> #   relations <chr>, geodeticDatum <chr>, class <chr>, countryCode <chr>,
#> #   country <chr>, identifier <chr>, created <chr>, gbifID <chr>,
#> #   occurrenceID <chr>, associatedSequences <chr>,
#> #   higherClassification <chr>, taxonID <chr>, sex <chr>,
#> #   establishmentMeans <chr>, continent <chr>, references <chr>,
#> #   institutionID <chr>, dynamicProperties <chr>, fieldNumber <chr>,
#> #   language <chr>, type <chr>, preparations <chr>, catalogNumber <chr>,
#> #   occurrenceStatus <chr>, institutionCode <chr>,
#> #   nomenclaturalCode <chr>, higherGeography <chr>,
#> #   verbatimEventDate <chr>, endDayOfYear <chr>,
#> #   georeferenceVerificationStatus <chr>, datasetName <chr>,
#> #   locality <chr>, collectionCode <chr>, verbatimLocality <chr>,
#> #   recordedBy <chr>,
#> #   http...unknown.org.http_..rs.tdwg.org.dwc.terms.ResourceRelationship <chr>,
#> #   otherCatalogNumbers <chr>, startDayOfYear <chr>, accessRights <chr>,
#> #   collectionID <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(search = "taxonKey", id = 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)
#> coord. ref. : +init=epsg:4326 +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 
#> data source : in memory
#> names       : layer 
#> values      : 0, 1  (min, max)
library(raster)
plot(x, axes = FALSE, box = FALSE)

map

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for rgbif in R doing citation(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.

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Contributors

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