Thursday, November 21, 2013 From rOpenSci (https://ropensci.org/blog/2013/11/21/rgbif-changes/). Except where otherwise noted, content on this site is licensed under the CC-BY license.
The Global Biodiversity Information Facility (GBIF) is a warehouse of species occurrence data - collecting data from a lot of different sources. Our package rgbif allows you to interact with GBIF from R. We interact with GBIF via their Application Programming Interface, or API. Our last version on CRAN (v0.3) interacted with the older version of their API - this version interacts with the new version of their API. However, we also retained functions that interact with the old API.
We have strived to have meaningful error messages for various arguments that have been changed, and for functions that were in v0.3, but now work with the new API (e.g. organizations, networks).
GBIF did a large overhaul of the interface, so the possible arguments to use in each function are quite different. Don’t hesitate to get in touch if you have a question! They have a set of methods to look up metadata about sources (under Registry), a set of methods for species names (under Species), a set of methods for occurrences (under Occurrences), and a set of methods for requesting tile map layers (under Maps). In rgbif we provide functions for the first three, Registry, Species, and Occurrences. We don’t provide R interfaces to their Maps service as it only makes sense to use in a web native workflow.
Tutorial for old GBIF API: /tutorials/rgbif_tutorial.html
Note: the Mac OSX binary is not available yet on CRAN…
install.packages("rgbif")
library(rgbif)
Look up specific datasets
out <- datasets(data = "contact", uuid = "a6998220-7e3a-485d-9cd6-73076bd85657")
library(plyr)
ldply(out, data.frame)[, c(1:4)] # just a few columns for brevity
## key type primary firstName
## 1 22901 ADMINISTRATIVE_POINT_OF_CONTACT TRUE Ian
## 2 22900 AUTHOR FALSE Graham
## 3 22899 METADATA_AUTHOR TRUE Ian
## 4 22898 ORIGINATOR TRUE Ian
Search datasets: Get all datasets tagged with keyword “france”.
out <- dataset_search(keyword = "france")
out$data
## title
## 1 Cartographie des Leguminosae (Fabaceae) en France
## 2 Carnet en Ligne
## 3 Phytochorologie des départements français
## 4 Actualisation de la cartographie des Ptéridophytes de France et d'Europe occidentale
## hostingOrganization owningOrganization type publishingCountry
## 1 Tela-Botanica Tela-Botanica OCCURRENCE FR
## 2 Tela-Botanica Tela-Botanica OCCURRENCE FR
## 3 Tela-Botanica Tela-Botanica OCCURRENCE FR
## 4 Tela-Botanica Tela-Botanica OCCURRENCE FR
## key
## 1 cbd241aa-a115-4856-af66-fac5cb90f2cc
## 2 baa86fb2-7346-4507-a34f-44e4c1bd0d57
## 3 2d680d46-d783-4ea7-94b1-2556cd653e36
## 4 2aaf8ea9-0460-41d2-a651-3583479947c6
## hostingOrganizationKey
## 1 b2dbd210-90c2-11df-86a3-b8a03c50a862
## 2 b2dbd210-90c2-11df-86a3-b8a03c50a862
## 3 b2dbd210-90c2-11df-86a3-b8a03c50a862
## 4 b2dbd210-90c2-11df-86a3-b8a03c50a862
## owningOrganizationKey
## 1 b2dbd210-90c2-11df-86a3-b8a03c50a862
## 2 b2dbd210-90c2-11df-86a3-b8a03c50a862
## 3 b2dbd210-90c2-11df-86a3-b8a03c50a862
## 4 b2dbd210-90c2-11df-86a3-b8a03c50a862
Get dataset metrics
dataset_metrics(uuid = "3f8a1297-3259-4700-91fc-acc4170b27ce")$countByRank
## SPECIES GENUS VARIETY SUBSPECIES SECTION TRIBE
## 5924 1223 854 748 324 323
## SUBGENUS FAMILY SUBFAMILY SUBSECTION SUBTRIBE ORDER
## 194 171 147 59 57 55
## SERIES SUPERORDER SUBCLASS CLASS
## 40 12 6 2
nodes(data = "identifier", uuid = "1193638d-32d1-43f0-a855-8727c94299d8")
## [[1]]
## [[1]]$key
## [1] 13587
##
## [[1]]$type
## [1] "GBIF_PARTICIPANT"
##
## [[1]]$identifier
## [1] "57"
##
## [[1]]$createdBy
## [1] "registry-migration.gbif.org"
##
## [[1]]$created
## [1] "2013-10-24T09:06:08.312+0000"
out <- organizations(data = "contact", uuid = "4b4b2111-ee51-45f5-bf5e-f535f4a1c9dc")
ldply(out, data.frame)[, c(1:4)] # just a few columns for brevity
## key type primary
## 1 20006 ADMINISTRATIVE_POINT_OF_CONTACT TRUE
## 2 20007 TECHNICAL_POINT_OF_CONTACT TRUE
## 3 20008 TECHNICAL_POINT_OF_CONTACT FALSE
## firstName
## 1 Francisco Javier Bonet García
## 2 Antonio Jesús Pérez Luque
## 3 Ramon Perez Perez
out <- name_backbone(name = "Helianthus", rank = "genus", kingdom = "plants")
out$phylum
## [1] "Magnoliophyta"
data.frame(out) # as a data.frame
## usageKey scientificName canonicalName rank synonym confidence matchType
## 1 3119134 Helianthus L. Helianthus GENUS FALSE 97 EXACT
## kingdom phylum clazz order family genus
## 1 Plantae Magnoliophyta Magnoliopsida Asterales Asteraceae Helianthus
## kingdomKey phylumKey classKey orderKey familyKey genusKey
## 1 6 49 220 414 3065 3119134
out <- name_lookup(query = "Cnaemidophor", rank = "genus")
head(out$data)
## key nubKey parentKey parent kingdom phylum clazz
## 1 116755723 1858636 110614854 Pterophoridae Animalia Arthropoda Insecta
## 2 1858636 1858636 8863 Pterophoridae Animalia Arthropoda Insecta
## 3 124531302 1858636 NA <NA> <NA> <NA> <NA>
## 4 101053441 1858636 100725398 Pterophoridae Animalia Arthropoda Insecta
## 5 126862804 1858636 126783981 Pterophoridae Animalia Arthropoda Insecta
## 6 107119486 1858636 107119872 Pterophoridae <NA> <NA> <NA>
## order family genus kingdomKey phylumKey classKey
## 1 Lepidoptera Pterophoridae Cnaemidophorus 116630539 116762374 116686069
## 2 Lepidoptera Pterophoridae Cnaemidophorus 1 54 216
## 3 <NA> <NA> Cnaemidophorus NA NA NA
## 4 Lepidoptera Pterophoridae Cnaemidophorus 101719444 102545136 101674726
## 5 Lepidoptera Pterophoridae Cnaemidophorus 126774927 126774928 126775138
## 6 <NA> Pterophoridae Cnaemidophorus NA NA NA
## orderKey familyKey genusKey canonicalName authorship nameType
## 1 116843281 110614854 116755723 Cnaemidophorus Wallengren, 1862 WELLFORMED
## 2 797 8863 1858636 Cnaemidophorus Wallengren, 1862 WELLFORMED
## 3 NA NA 124531302 Cnaemidophorus WELLFORMED
## 4 102306154 100725398 101053441 Cnaemidophorus Wallengren, 1860 WELLFORMED
## 5 126775421 126783981 126862804 Cnaemidophorus WELLFORMED
## 6 NA 107119872 107119486 Cnaemidophorus Wallengren, 1862 WELLFORMED
## rank numOccurrences
## 1 GENUS 0
## 2 GENUS 0
## 3 GENUS 0
## 4 GENUS 0
## 5 GENUS 0
## 6 GENUS 0
ldply(name_usage(key = 3119195, data = "vernacular_names")$results, data.frame)
## key usageKey datasetKey vernacularName
## 1 512055 117075019 244609a2-e92e-4465-bc9c-f3faa8ce0fcc Common sunflower
## 2 267381 117214133 134eca5f-65ab-49a2-a229-3d0d35fcbefe Common sunflower
## 3 786116 125790787 16c3f9cb-4b19-4553-ac8e-ebb90003aa02 Sonnenblume
## 4 496979 106239436 fab88965-e69d-4491-a04d-e3198b626e52 common sunflower
## 5 750838 124893865 705922f7-5ba5-49ab-a75d-722e3090e690 common sunflower
## 6 38463 100019171 3f8a1297-3259-4700-91fc-acc4170b27ce common sunflower
## 7 38464 100019171 3f8a1297-3259-4700-91fc-acc4170b27ce garden sunflower
## 8 38465 100019171 3f8a1297-3259-4700-91fc-acc4170b27ce grand soleil
## 9 38466 100019171 3f8a1297-3259-4700-91fc-acc4170b27ce hélianthe annuel
## 10 38467 100019171 3f8a1297-3259-4700-91fc-acc4170b27ce soleil
## 11 267382 117214133 134eca5f-65ab-49a2-a229-3d0d35fcbefe sunflower
## 12 512056 117075019 244609a2-e92e-4465-bc9c-f3faa8ce0fcc sunflower
## 13 38468 100019171 3f8a1297-3259-4700-91fc-acc4170b27ce tournesol
## 14 291752 116845199 cbb6498e-8927-405a-916b-576d00a6289b Подсолнечник
## 15 637567 110853779 1ec61203-14fa-4fbd-8ee5-a4a80257b45a 向日葵
## language preferred
## 1 ENGLISH FALSE
## 2 ENGLISH FALSE
## 3 GERMAN FALSE
## 4 UNKNOWN FALSE
## 5 ENGLISH FALSE
## 6 ENGLISH FALSE
## 7 ENGLISH FALSE
## 8 FRENCH FALSE
## 9 FRENCH FALSE
## 10 FRENCH FALSE
## 11 ENGLISH FALSE
## 12 ENGLISH FALSE
## 13 FRENCH FALSE
## 14 RUSSIAN FALSE
## 15 CHINESE FALSE
This is meant to be a quick name suggestion function that returns up to 20 names by doing prefix matching against the scientific name. Results are ordered by relevance.
name_suggest(q = "Puma", fields = c("key", "canonicalName"))
## key canonicalName
## 1 2435098 Puma
## 2 2435099 Puma concolor
## 3 2435146 Puma yagouaroundi
## 4 4969803 Puma lacustris
## 5 6164589 Puma concolor anthonyi
## 6 6164590 Puma concolor couguar
## 7 6164591 Puma concolor kaibabensis
## 8 6164592 Puma concolor oregonensis
## 9 6164594 Puma concolor vancouverensis
## 10 6164599 Puma concolor azteca
## 11 6164600 Puma concolor coryi
## 12 6164602 Puma concolor improcera
## 13 6164603 Puma concolor missoulensis
## 14 6164604 Puma concolor stanleyana
## 15 6164608 Puma concolor californica
## 16 6164610 Puma concolor hippolestes
## 17 6164611 Puma concolor mayensis
## 18 6164613 Puma concolor schorgeri
## 19 6164618 Puma concolor browni
## 20 6164620 Puma concolor cougar
occ_count(nubKey = 2435099, georeferenced = TRUE)
## [1] 2541
occ_get(key = c(773433533, 101010, 240713150, 855998194, 49819470), return = "data")
## name key longitude latitude
## 1 Helianthus annuus L. 773433533 -117.00 32.85
## 2 Platydoras costatus (Linnaeus, 1758) 101010 -70.07 -4.35
## 3 Pelosina 240713150 163.58 -77.57
## 4 Sciurus vulgaris Linnaeus, 1758 855998194 12.04 58.41
## 5 Phlogophora meticulosa Linnaeus, 1758 49819470 13.28 55.72
This is the most common function you may use in rgbif.
key <- name_backbone(name = "Helianthus annuus", kingdom = "plants")$speciesKey
occ_search(taxonKey = key, limit = 2)
## $meta
## $meta$offset
## [1] 0
##
## $meta$limit
## [1] 2
##
## $meta$endOfRecords
## [1] FALSE
##
## $meta$count
## [1] 18190
##
##
## $hierarchy
## $hierarchy[[1]]
## name key rank
## 1 Plantae 6 kingdom
## 2 Magnoliophyta 49 phylum
## 3 Magnoliopsida 220 clazz
## 4 Asterales 414 order
## 5 Asteraceae 3065 family
## 6 Helianthus 3119134 genus
## 7 Helianthus annuus L. 3119195 species
##
##
## $data
## name key longitude latitude
## 1 Helianthus annuus L. 773433533 -117.00 32.85
## 2 Helianthus annuus L. 855868468 16.42 56.58
Another example, using Well Known Text Area as a bounding polygon to search on
occ_search(geometry = "POLYGON((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1))")$data
## name key longitude
## 1 Carcharhinus albimarginatus (Ruppell, 1837) 8.57e+08 34.86
## 2 Goniobranchus tinctorius (Rüppell & Leuckart, 1828) 8.57e+08 33.92
## 3 Megalomma vesiculosum (Montagu, 1815) 8.57e+08 23.98
## 4 Thalassoma lunare (Linnaeus, 1758) 8.57e+08 33.92
## 5 Hermodice carunculata (Pallas, 1766) 8.57e+08 23.98
## 6 Pterois volitans (Linnaeus, 1758) 8.57e+08 33.92
## 7 Marthasterias glacialis (Linnaeus, 1758) 8.57e+08 23.98
## 8 Epinephelus marginatus (Lowe, 1834) 8.57e+08 23.98
## 9 Scorpaenopsis diabolus (Cuvier, 1829) 8.57e+08 33.92
## 10 Muraena helena Linnaeus, 1758 8.57e+08 23.98
## 11 Gobius bucchichi Steindachner, 1870 8.57e+08 23.98
## 12 Thalassoma purpureum (Forsskål, 1775) 8.57e+08 33.92
## 13 Bothus podas (Delaroche, 1809) 8.57e+08 23.98
## 14 Symphodus tinca (Linnaeus, 1758) 8.57e+08 34.07
## 15 Pagrus pagrus (Linnaeus, 1758) 8.57e+08 34.07
## 16 Sargocentron rubrum (Forsskål, 1775) 8.57e+08 34.07
## 17 Marthasterias glacialis (Linnaeus, 1758) 8.57e+08 23.98
## 18 Spongia officinalis Linnaeus, 1759 8.57e+08 23.98
## 19 Hermodice carunculata (Pallas, 1766) 8.57e+08 23.98
## 20 Octopus hubbsorum Berry, 1953 8.57e+08 23.98
## latitude
## 1 25.31
## 2 27.36
## 3 37.66
## 4 27.36
## 5 37.66
## 6 27.36
## 7 37.66
## 8 37.66
## 9 27.36
## 10 37.66
## 11 37.66
## 12 27.36
## 13 37.66
## 14 35.00
## 15 35.00
## 16 35.00
## 17 37.66
## 18 37.66
## 19 37.66
## 20 37.66
