Seach and retrieve data from the Global Biodiverity Information Facilty (GBIF)
About the package
rgbif is an R package to search and retrieve data from the Global Biodiverity Information Facilty (GBIF). rgbif wraps R code around the GBIF API to allow you to talk to GBIF from R.
Get rgbif
Install from CRAN
install.packages("rgbif")
Or install the development version from GitHub
remotes::install_github("ropensci/rgbif")
Load rgbif
Number of occurrences
Search by type of record, all observational in this case
occ_count(basisOfRecord='OBSERVATION') #> [1] 18911003
Records for Puma concolor with lat/long data (georeferened) only. Note that hasCoordinate in occ_search() is the same as georeferenced in occ_count().
occ_count(taxonKey=2435099, georeferenced=TRUE) #> [1] 7165
All georeferenced records in GBIF
occ_count(georeferenced=TRUE) #> [1] 1532830619
Records from Denmark
denmark_code <- isocodes[grep("Denmark", isocodes$name), "code"] occ_count(country=denmark_code) #> [1] 42078239
Number of records in a particular dataset
occ_count(datasetKey='9e7ea106-0bf8-4087-bb61-dfe4f29e0f17') #> [1] 4591
All records from 2012
occ_count(year=2012) #> [1] 62152590
Records for a particular dataset, and only for preserved specimens
occ_count(datasetKey='e707e6da-e143-445d-b41d-529c4a777e8b', basisOfRecord='OBSERVATION') #> [1] 0
Search for taxon names
Get possible values to be used in taxonomic rank arguments in functions
taxrank() #> [1] "kingdom" "phylum" "class" "order" #> [5] "family" "genus" "species" "subspecies" #> [9] "infraspecific"
name_lookup() does full text search of name usages covering the scientific and vernacular name, the species description, distribution and the entire classification across all name usages of all or some checklists. Results are ordered by relevance as this search usually returns a lot of results.
By default name_lookup() returns five slots of information: meta, data, facets, hierarchies, and names. hierarchies and names elements are named by their matching GBIF key in the data.frame in the data slot.
out <- name_lookup(query='mammalia')
names(out) #> [1] "meta" "data" "facets" "hierarchies" "names"
out$meta #> # A tibble: 1 x 4 #> offset limit endOfRecords count #> <int> <int> <lgl> <int> #> 1 0 100 FALSE 2042
head(out$data) #> # A tibble: 6 x 28 #> key scientificName datasetKey nubKey parentKey parent kingdom phylum #> <int> <chr> <chr> <int> <int> <chr> <chr> <chr> #> 1 1.14e8 Mammalia 8dc469b3-… 359 114068664 Verte… Animal… Chord… #> 2 1.57e8 Mammalia 081304be-… 359 157251235 Chord… Animal… Chord… #> 3 1.44e8 Mammalia bc3553e8-… 359 144211912 Chord… Animal… Chord… #> 4 3.59e2 Mammalia d7dddbf4-… NA 44 Chord… Animal… Chord… #> 5 1.35e8 Mammalia 0a423169-… 359 135216355 Chord… Animal… Chord… #> 6 1.52e8 Mammalia 4b4931d6-… 359 152182137 Chord… Animal… Chord… #> # … with 20 more variables: kingdomKey <int>, phylumKey <int>, classKey <int>, #> # canonicalName <chr>, authorship <chr>, nameType <chr>, #> # taxonomicStatus <chr>, rank <chr>, origin <chr>, numDescendants <int>, #> # numOccurrences <int>, habitats <chr>, nomenclaturalStatus <lgl>, #> # threatStatuses <chr>, synonym <lgl>, class <chr>, constituentKey <chr>, #> # extinct <lgl>, publishedIn <chr>, taxonID <chr>
out$facets #> NULL
out$hierarchies[1:2] #> $`114068957` #> rankkey name #> 1 114067672 Animalia #> 2 114068658 Chordata #> 3 114068664 Vertebrata #> #> $`157251236` #> rankkey name #> 1 157251234 Animalia #> 2 157251235 Chordata
out$names[2] #> $`168001908` #> vernacularName language #> 1 njiccehasat sme
Search for a genus
z <- name_lookup(query='Cnaemidophorus', rank="genus") z$data #> # A tibble: 22 x 35 #> key scientificName datasetKey nubKey parentKey parent kingdom phylum #> <int> <chr> <chr> <int> <int> <chr> <chr> <chr> #> 1 1.68e8 Cnaemidophorus cbb6498e-… 1858636 168457560 Ptero… Animal… Arthr… #> 2 1.24e8 Cnaemidophorus fab88965-… NA 104446806 Ptero… Metazoa Arthr… #> 3 1.68e8 Cnaemidophorus 16c3f9cb-… 1858636 100557623 Ptero… <NA> <NA> #> 4 1.69e8 Cnaemidophorus 4dd32523-… 1858636 168800971 Ptero… Animal… Arthr… #> 5 1.56e8 Cnaemidophorus 7ddf754f-… 1858636 155857752 Ptero… Animal… Arthr… #> 6 1.58e8 Cnaemidophorus 4cec8fef-… 1858636 157904443 Ptero… Animal… Arthr… #> 7 1.69e8 Cnaemidophorus 4b3e4a71-… 1858636 168525701 Ptero… Animal… Arthr… #> 8 1.59e8 Cnaemidophorus 23905003-… 1858636 159439401 Ptero… Animal… Arthr… #> 9 1.69e8 Cnaemidophorus 848271aa-… 1858636 168992508 Lepid… Animal… <NA> #> 10 1.23e8 Cnaemidophoru… 90d9e8a6-… 1858636 123394987 Ptero… Animal… Arthr… #> # … with 12 more rows, and 27 more variables: order <chr>, family <chr>, #> # genus <chr>, kingdomKey <int>, phylumKey <int>, classKey <int>, #> # orderKey <int>, familyKey <int>, genusKey <int>, canonicalName <chr>, #> # taxonomicStatus <chr>, rank <chr>, origin <chr>, numDescendants <int>, #> # numOccurrences <int>, habitats <lgl>, nomenclaturalStatus <chr>, #> # threatStatuses <chr>, synonym <lgl>, class <chr>, nameType <chr>, #> # taxonID <chr>, authorship <chr>, accordingTo <chr>, constituentKey <chr>, #> # publishedIn <chr>, extinct <lgl>
Search for the class mammalia
w <- name_lookup(query='mammalia') w$data #> # A tibble: 100 x 28 #> key scientificName datasetKey nubKey parentKey parent kingdom phylum #> <int> <chr> <chr> <int> <int> <chr> <chr> <chr> #> 1 1.14e8 Mammalia 8dc469b3-… 359 114068664 Verte… Animal… Chord… #> 2 1.57e8 Mammalia 081304be-… 359 157251235 Chord… Animal… Chord… #> 3 1.44e8 Mammalia bc3553e8-… 359 144211912 Chord… Animal… Chord… #> 4 3.59e2 Mammalia d7dddbf4-… NA 44 Chord… Animal… Chord… #> 5 1.35e8 Mammalia 0a423169-… 359 135216355 Chord… Animal… Chord… #> 6 1.52e8 Mammalia 4b4931d6-… 359 152182137 Chord… Animal… Chord… #> 7 1.42e8 Mammalia 90e4f0e7-… 359 142234654 Chord… Animal… Chord… #> 8 1.35e8 Mammalia 5acbd076-… 359 134996932 Chord… Animal… Chord… #> 9 1.68e8 Mammalia a6c6cead-… 359 168001717 Verte… Animal… Chord… #> 10 1.59e8 Mammalia b2a18f87-… 359 159454905 Chord… Animal… Chord… #> # … with 90 more rows, and 20 more variables: kingdomKey <int>, #> # phylumKey <int>, classKey <int>, canonicalName <chr>, authorship <chr>, #> # nameType <chr>, taxonomicStatus <chr>, rank <chr>, origin <chr>, #> # numDescendants <int>, numOccurrences <int>, habitats <chr>, #> # nomenclaturalStatus <lgl>, threatStatuses <chr>, synonym <lgl>, #> # class <chr>, constituentKey <chr>, extinct <lgl>, publishedIn <chr>, #> # taxonID <chr>
Look up the species Helianthus annuus
m <- name_lookup(query = 'Helianthus annuus', rank="species") m$data #> # A tibble: 100 x 40 #> key scientificName datasetKey nubKey parentKey parent kingdom phylum #> <int> <chr> <chr> <int> <int> <chr> <chr> <chr> #> 1 1.15e8 Helianthus an… ee2aac07-… 9206251 144238801 Helia… Plantae Trach… #> 2 1.35e8 Helianthus an… f82a4f7f-… 9206251 167773411 Aster… Plantae Trach… #> 3 1.35e8 Helianthus an… 29d2d5a6-… 9206251 168341218 Aster… Plantae Trach… #> 4 1.28e8 Helianthus an… 41c06f1a-… 9206251 146770884 Amara… Plantae <NA> #> 5 1.46e8 Helianthus an… 6a97172b-… 9206251 147653302 Helia… <NA> <NA> #> 6 1.63e8 Helianthus an… 88217638-… 9206251 163398972 Aster… Plantae Trach… #> 7 1.35e8 Helianthus an… 83ca3188-… 9206251 168210720 Aster… Plantae Trach… #> 8 1.46e8 Helianthus an… 3f5e930b-… 9206251 157140516 Helia… Plantae Angio… #> 9 1.03e8 Helianthus an… fab88965-… NA 103340270 Helia… Viridi… Strep… #> 10 1.60e8 Helianthus an… 39f36f10-… 9206251 164560273 Helia… Plantae Magno… #> # … with 90 more rows, and 32 more variables: order <chr>, family <chr>, #> # genus <chr>, species <chr>, kingdomKey <int>, phylumKey <int>, #> # classKey <int>, orderKey <int>, familyKey <int>, genusKey <int>, #> # speciesKey <int>, canonicalName <chr>, authorship <chr>, nameType <chr>, #> # taxonomicStatus <chr>, rank <chr>, origin <chr>, numDescendants <int>, #> # numOccurrences <int>, habitats <chr>, nomenclaturalStatus <chr>, #> # threatStatuses <chr>, synonym <lgl>, class <chr>, taxonID <chr>, #> # acceptedKey <int>, accepted <chr>, constituentKey <chr>, accordingTo <chr>, #> # publishedIn <chr>, basionymKey <int>, basionym <chr>
The function name_usage() works with lots of different name endpoints in GBIF, listed at https://www.gbif.org/developer/species#nameUsages
name_usage(key=3119195, language="FRENCH", data='vernacularNames') #> Records returned [0] #> Args [offset=0, limit=100, language=FRENCH] #> # A tibble: 0 x 0
The function name_backbone() is used to search against the GBIF backbone taxonomy
name_backbone(name='Helianthus', rank='genus', kingdom='plants') #> # A tibble: 1 x 20 #> usageKey scientificName canonicalName rank status confidence matchType #> * <int> <chr> <chr> <chr> <chr> <int> <chr> #> 1 3119134 Helianthus L. Helianthus GENUS ACCEP… 97 EXACT #> # … with 13 more variables: kingdom <chr>, phylum <chr>, order <chr>, #> # family <chr>, genus <chr>, kingdomKey <int>, phylumKey <int>, #> # classKey <int>, orderKey <int>, familyKey <int>, genusKey <int>, #> # synonym <lgl>, class <chr>
The function name_suggest() is optimized for speed, and gives back suggested names based on query parameters.
head( name_suggest(q='Puma concolor') ) #> $data #> # A tibble: 33 x 3 #> key canonicalName rank #> <int> <chr> <chr> #> 1 2435099 Puma concolor SPECIES #> 2 8860878 Puma concolor capricornensis SUBSPECIES #> 3 6164618 Puma concolor browni SUBSPECIES #> 4 8951716 Puma concolor borbensis SUBSPECIES #> 5 6164599 Puma concolor azteca SUBSPECIES #> 6 8916934 Puma concolor bangsi SUBSPECIES #> 7 6164622 Puma concolor puma SUBSPECIES #> 8 6164604 Puma concolor stanleyana SUBSPECIES #> 9 6164610 Puma concolor hippolestes SUBSPECIES #> 10 6164620 Puma concolor cougar SUBSPECIES #> # … with 23 more rows #> #> $hierarchy #> list()
Single occurrence records
Get data for a single occurrence. Note that data is returned as a list, with slots for metadata and data.
occ_get(key=855998194) #> [[1]] #> [[1]]$hierarchy #> name key rank #> 1 Animalia 1 kingdom #> 2 Chordata 44 phylum #> 3 Mammalia 359 class #> 4 Rodentia 1459 order #> 5 Sciuridae 9456 family #> 6 Sciurus 2437489 genus #> 7 Sciurus vulgaris 8211070 species #> #> [[1]]$media #> [[1]]$media$`855998194` #> [[1]]$media$`855998194`[[1]] #> [[1]]$media$`855998194`[[1]][[1]] #> [1] "none" #> #> #> [[1]]$media$`855998194`$key #> [1] "855998194" #> #> [[1]]$media$`855998194`$species #> [1] "Sciurus vulgaris" #> #> [[1]]$media$`855998194`$decimalLatitude #> [1] 58.40677 #> #> [[1]]$media$`855998194`$decimalLongitude #> [1] 12.04386 #> #> [[1]]$media$`855998194`$country #> [1] "Sweden" #> #> #> #> [[1]]$data #> key scientificName decimalLatitude decimalLongitude #> 1 855998194 Sciurus vulgaris Linnaeus, 1758 58.40677 12.04386 #> issues #> 1 cdround,gass84
Get many occurrences. occ_get is vectorized
occ_get(key=c(855998194, 240713150)) #> [[1]] #> [[1]]$hierarchy #> name key rank #> 1 Animalia 1 kingdom #> 2 Chordata 44 phylum #> 3 Mammalia 359 class #> 4 Rodentia 1459 order #> 5 Sciuridae 9456 family #> 6 Sciurus 2437489 genus #> 7 Sciurus vulgaris 8211070 species #> #> [[1]]$media #> [[1]]$media$`855998194` #> [[1]]$media$`855998194`[[1]] #> [[1]]$media$`855998194`[[1]][[1]] #> [1] "none" #> #> #> [[1]]$media$`855998194`$key #> [1] "855998194" #> #> [[1]]$media$`855998194`$species #> [1] "Sciurus vulgaris" #> #> [[1]]$media$`855998194`$decimalLatitude #> [1] 58.40677 #> #> [[1]]$media$`855998194`$decimalLongitude #> [1] 12.04386 #> #> [[1]]$media$`855998194`$country #> [1] "Sweden" #> #> #> #> [[1]]$data #> key scientificName decimalLatitude decimalLongitude #> 1 855998194 Sciurus vulgaris Linnaeus, 1758 58.40677 12.04386 #> issues #> 1 cdround,gass84 #> #> #> [[2]] #> [[2]]$hierarchy #> name key rank #> 1 Chromista 4 kingdom #> 2 Foraminifera 8376456 phylum #> 3 Monothalamea 7882876 class #> 4 Astrorhizida 8142878 order #> 5 Astrorhizidae 7747923 family #> 6 Pelosina 7822114 genus #> #> [[2]]$media #> [[2]]$media$`240713150` #> [[2]]$media$`240713150`[[1]] #> [[2]]$media$`240713150`[[1]][[1]] #> [1] "none" #> #> #> [[2]]$media$`240713150`$key #> [1] "240713150" #> #> [[2]]$media$`240713150`$decimalLatitude #> [1] -77.5667 #> #> [[2]]$media$`240713150`$decimalLongitude #> [1] 163.583 #> #> [[2]]$media$`240713150`$country #> [1] "Antarctica" #> #> #> #> [[2]]$data #> key scientificName decimalLatitude decimalLongitude issues #> 1 240713150 Pelosina Brady, 1879 -77.5667 163.583 gass84
Search for occurrences
Note: The maximum number of records you can get with occ_search() and occ_data() is 100,000. See https://www.gbif.org/developer/occurrence
By default occ_search() returns a dplyr like output summary in which the data printed expands based on how much data is returned, and the size of your window. You can search by scientific name:
occ_search(scientificName = "Ursus americanus", limit = 20) #> Records found [18984] #> Records returned [20] #> No. unique hierarchies [1] #> No. media records [20] #> No. facets [0] #> Args [limit=20, offset=0, scientificName=Ursus americanus, fields=all] #> # A tibble: 20 x 83 #> 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-… #> 11 2557… Ursus america… 46.1 -87.4 cdrou… 50c9509d-… #> 12 2563… Ursus america… 34.4 -118. cdrou… 50c9509d-… #> 13 2563… Ursus america… 35.9 -121. cdrou… 50c9509d-… #> 14 2563… Ursus america… 35.9 -121. cdrou… 50c9509d-… #> 15 2563… Ursus america… 35.9 -121. cdrou… 50c9509d-… #> 16 2563… Ursus america… 35.9 -121. cdrou… 50c9509d-… #> 17 2563… Ursus america… 35.5 -82.6 cdrou… 50c9509d-… #> 18 2563… Ursus america… 35.1 -118. cdrou… 50c9509d-… #> 19 2563… Ursus america… 29.2 -103. cdrou… 50c9509d-… #> 20 2563… Ursus america… 42.5 -123. cdrou… 50c9509d-… #> # … with 77 more variables: publishingOrgKey <chr>, installationKey <chr>, #> # publishingCountry <chr>, protocol <chr>, lastCrawled <chr>, #> # lastParsed <chr>, crawlId <int>, extensions <chr>, basisOfRecord <chr>, #> # occurrenceStatus <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>, gadm.level0.gid <chr>, #> # gadm.level0.name <chr>, gadm.level1.gid <chr>, gadm.level1.name <chr>, #> # gadm.level2.gid <chr>, gadm.level2.name <chr>, geodeticDatum <chr>, #> # class <chr>, countryCode <chr>, recordedByIDs <chr>, identifiedByIDs <chr>, #> # country <chr>, rightsHolder <chr>, identifier <chr>, #> # http...unknown.org.nick <chr>, verbatimEventDate <chr>, datasetName <chr>, #> # gbifID <chr>, collectionCode <chr>, verbatimLocality <chr>, #> # occurrenceID <chr>, taxonID <chr>, recordedBy <chr>, catalogNumber <chr>, #> # http...unknown.org.occurrenceDetails <chr>, institutionCode <chr>, #> # rights <chr>, eventTime <chr>, identifiedBy <chr>, identificationID <chr>, #> # name <chr>, informationWithheld <chr>, occurrenceRemarks <chr>
Or to be more precise, you can search for names first, make sure you have the right name, then pass the GBIF key to the occ_search() function:
key <- name_suggest(q='Helianthus annuus', rank='species')$key[1] occ_search(taxonKey=key, limit=20) #> Records found [1631169502] #> Records returned [20] #> No. unique hierarchies [18] #> No. media records [20] #> No. facets [0] #> Args [limit=20, offset=0, fields=all] #> # A tibble: 20 x 108 #> key scientificName issues datasetKey publishingOrgKey installationKey #> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 1039… Psittacus eri… "osii… 854cf79e-… 2e167bb0-4441-1… 3f28c5e9-59b3-… #> 2 1086… Asplenium rad… "gass… a51fa32f-… f6e2efc9-42a3-4… b38ff2b7-c8af-… #> 3 1095… Eugenia pyrif… "" 3b8e9d83-… ab5c0b99-5af3-4… b38ff2b7-c8af-… #> 4 1135… Marasmius epi… "" 0afba960-… 58520c30-bafb-1… 602f7766-f762-… #> 5 1135… Berkleasmium … "" 0afba960-… 58520c30-bafb-1… 602f7766-f762-… #> 6 1135… Pseudovalsa u… "" 0afba960-… 58520c30-bafb-1… 602f7766-f762-… #> 7 1135… Hemitrichia i… "" 0afba960-… 58520c30-bafb-1… 602f7766-f762-… #> 8 1830… Diatrypella f… "" 0afba960-… 58520c30-bafb-1… 602f7766-f762-… #> 9 1830… Cryptocline t… "" 0afba960-… 58520c30-bafb-1… 602f7766-f762-… #> 10 1840… Asota helicon… "osii… e0b8cb67-… 7c07cec1-2925-4… 08eefeeb-e20f-… #> 11 1840… Selepa Moore,… "osii… e0b8cb67-… 7c07cec1-2925-4… 08eefeeb-e20f-… #> 12 1841… Lemyra impari… "txma… e0b8cb67-… 7c07cec1-2925-4… 08eefeeb-e20f-… #> 13 1880… Limnonectes w… "gass… dce00a1f-… b554c320-0560-1… c7b49e46-602a-… #> 14 1880… Limnonectes w… "gass… dce00a1f-… b554c320-0560-1… c7b49e46-602a-… #> 15 1880… Limnonectes w… "gass… dce00a1f-… b554c320-0560-1… c7b49e46-602a-… #> 16 1897… Polystichum w… "cdro… 83ae84cf-… 32e82a64-c9b4-4… 58f76e14-f21d-… #> 17 1897… Hymenophyllum… "mulu… 83ae84cf-… 32e82a64-c9b4-4… 58f76e14-f21d-… #> 18 1897… Epacris pauci… "cdro… 83ae84cf-… 32e82a64-c9b4-4… 58f76e14-f21d-… #> 19 1897… Metrosideros … "cdro… 83ae84cf-… 32e82a64-c9b4-4… 58f76e14-f21d-… #> 20 1897… Coprosma dodo… "mulu… 83ae84cf-… 32e82a64-c9b4-4… 58f76e14-f21d-… #> # … with 102 more variables: publishingCountry <chr>, protocol <chr>, #> # lastCrawled <chr>, lastParsed <chr>, crawlId <int>, extensions <chr>, #> # basisOfRecord <chr>, individualCount <int>, occurrenceStatus <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>, eventDate <chr>, #> # modified <chr>, lastInterpreted <chr>, references <chr>, license <chr>, #> # identifiers <chr>, facts <chr>, relations <chr>, gadm <chr>, class <chr>, #> # recordedByIDs <chr>, identifiedByIDs <chr>, rightsHolder <chr>, #> # identifier <chr>, nomenclaturalCode <chr>, gbifID <chr>, #> # collectionCode <chr>, language <chr>, occurrenceID <chr>, type <chr>, #> # taxonRemarks <chr>, preparations <chr>, disposition <chr>, #> # recordedBy <chr>, catalogNumber <chr>, vernacularName <chr>, #> # previousIdentifications <chr>, institutionCode <chr>, #> # ownerInstitutionCode <chr>, datasetID <chr>, occurrenceRemarks <chr>, #> # bibliographicCitation <chr>, accessRights <chr>, #> # higherClassification <chr>, name <chr>, decimalLatitude <dbl>, #> # decimalLongitude <dbl>, dateIdentified <chr>, elevation <dbl>, #> # elevationAccuracy <dbl>, stateProvince <chr>, day <int>, #> # gadm.level0.gid <chr>, gadm.level0.name <chr>, gadm.level1.gid <chr>, #> # gadm.level1.name <chr>, gadm.level2.gid <chr>, gadm.level2.name <chr>, #> # gadm.level3.gid <chr>, gadm.level3.name <chr>, geodeticDatum <chr>, #> # countryCode <chr>, country <chr>, recordNumber <chr>, municipality <chr>, #> # locality <chr>, datasetName <chr>, identifiedBy <chr>, continent <chr>, #> # typifiedName <chr>, lifeStage <chr>, infraspecificEpithet <chr>, #> # county <chr>, associatedReferences <chr>, verbatimElevation <chr>, #> # higherGeography <chr>, institutionID <chr>, island <chr>, #> # islandGroup <chr>, …
You can index to different parts of the oupu; here, the metadata:
occ_search(taxonKey=key)$meta #> $offset #> [1] 300 #> #> $limit #> [1] 200 #> #> $endOfRecords #> [1] FALSE #> #> $count #> [1] 1631169502
You can choose what fields to return. This isn’t passed on to the API query to GBIF as they don’t allow that, but we filter out the columns before we give the data back to you.
occ_search(scientificName = "Ursus americanus", fields=c('name','basisOfRecord','protocol'), limit = 20) #> Records found [18984] #> Records returned [20] #> No. unique hierarchies [1] #> No. media records [20] #> No. facets [0] #> Args [limit=20, offset=0, scientificName=Ursus americanus, #> fields=name,basisOfRecord,protocol] #> # A tibble: 20 x 2 #> protocol basisOfRecord #> <chr> <chr> #> 1 DWC_ARCHIVE HUMAN_OBSERVATION #> 2 DWC_ARCHIVE HUMAN_OBSERVATION #> 3 DWC_ARCHIVE HUMAN_OBSERVATION #> 4 DWC_ARCHIVE HUMAN_OBSERVATION #> 5 DWC_ARCHIVE HUMAN_OBSERVATION #> 6 DWC_ARCHIVE HUMAN_OBSERVATION #> 7 DWC_ARCHIVE HUMAN_OBSERVATION #> 8 DWC_ARCHIVE HUMAN_OBSERVATION #> 9 DWC_ARCHIVE HUMAN_OBSERVATION #> 10 DWC_ARCHIVE HUMAN_OBSERVATION #> 11 DWC_ARCHIVE HUMAN_OBSERVATION #> 12 DWC_ARCHIVE HUMAN_OBSERVATION #> 13 DWC_ARCHIVE HUMAN_OBSERVATION #> 14 DWC_ARCHIVE HUMAN_OBSERVATION #> 15 DWC_ARCHIVE HUMAN_OBSERVATION #> 16 DWC_ARCHIVE HUMAN_OBSERVATION #> 17 DWC_ARCHIVE HUMAN_OBSERVATION #> 18 DWC_ARCHIVE HUMAN_OBSERVATION #> 19 DWC_ARCHIVE HUMAN_OBSERVATION #> 20 DWC_ARCHIVE HUMAN_OBSERVATION
Most parameters are vectorized, so you can pass in more than one value:
splist <- c('Cyanocitta stelleri', 'Junco hyemalis', 'Aix sponsa') keys <- sapply(splist, function(x) name_suggest(x)$key[1], USE.NAMES=FALSE) occ_search(taxonKey=keys, limit=5) #> Records found [NULL (1631169502), NULL (1631169502), NULL (1631169502)] #> Records returned [NULL (5), NULL (5), NULL (5)] #> No. unique hierarchies [NULL (5), NULL (5), NULL (5)] #> No. media records [NULL (5), NULL (5), NULL (5)] #> No. facets [NULL (0), NULL (0), NULL (0)] #> Args [limit=5, offset=0, taxonKey=NULL,NULL,NULL, fields=all] #> 3 requests; First 10 rows of data from NULL #> #> # A tibble: 5 x 97 #> key scientificName issues datasetKey publishingOrgKey installationKey #> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 1039… Psittacus eri… "osii… 854cf79e-… 2e167bb0-4441-1… 3f28c5e9-59b3-… #> 2 1086… Asplenium rad… "gass… a51fa32f-… f6e2efc9-42a3-4… b38ff2b7-c8af-… #> 3 1095… Eugenia pyrif… "" 3b8e9d83-… ab5c0b99-5af3-4… b38ff2b7-c8af-… #> 4 1135… Marasmius epi… "" 0afba960-… 58520c30-bafb-1… 602f7766-f762-… #> 5 1135… Berkleasmium … "" 0afba960-… 58520c30-bafb-1… 602f7766-f762-… #> # … with 91 more variables: publishingCountry <chr>, protocol <chr>, #> # lastCrawled <chr>, lastParsed <chr>, crawlId <int>, extensions <chr>, #> # basisOfRecord <chr>, individualCount <int>, occurrenceStatus <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>, eventDate <chr>, #> # modified <chr>, lastInterpreted <chr>, references <chr>, license <chr>, #> # identifiers <chr>, facts <chr>, relations <chr>, gadm <chr>, class <chr>, #> # recordedByIDs <chr>, identifiedByIDs <chr>, rightsHolder <chr>, #> # identifier <chr>, nomenclaturalCode <chr>, gbifID <chr>, #> # collectionCode <chr>, language <chr>, occurrenceID <chr>, type <chr>, #> # taxonRemarks <chr>, preparations <chr>, disposition <chr>, #> # recordedBy <chr>, catalogNumber <chr>, vernacularName <chr>, #> # previousIdentifications <chr>, institutionCode <chr>, #> # ownerInstitutionCode <chr>, datasetID <chr>, occurrenceRemarks <chr>, #> # bibliographicCitation <chr>, accessRights <chr>, #> # higherClassification <chr>, name <chr>, decimalLatitude <dbl>, #> # decimalLongitude <dbl>, dateIdentified <chr>, elevation <dbl>, #> # elevationAccuracy <dbl>, stateProvince <chr>, day <int>, #> # gadm.level0.gid <chr>, gadm.level0.name <chr>, gadm.level1.gid <chr>, #> # gadm.level1.name <chr>, gadm.level2.gid <chr>, gadm.level2.name <chr>, #> # gadm.level3.gid <chr>, gadm.level3.name <chr>, geodeticDatum <chr>, #> # countryCode <chr>, country <chr>, recordNumber <chr>, municipality <chr>, #> # locality <chr>, datasetName <chr>, identifiedBy <chr>, continent <chr>, #> # typifiedName <chr>
