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rgbif vignette - 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.

Install rgbif and dependencies

install.packages("rgbif")

Load rgbif and dependencies

library(rgbif)
library(XML)
library(RCurl)
library(plyr)
library(ggplot2)
library(maps)

Get number of occurrences for a set of search parameters

Search by type of record, all observational in this case

occ_count(basisOfRecord = "OBSERVATION")
[1] 286071783

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] 2604

All georeferenced records in GBIF

occ_count(georeferenced = TRUE)

[1] 376881077

Records from Denmark

occ_count(country = "DENMARK")
[1] 8628822

Records from France

occ_count(hostCountry = "FRANCE")
[1] 17272175

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] 31483292

Records for a particular dataset, and only for preserved specimens

occ_count(datasetKey = "8626bd3a-f762-11e1-a439-00145eb45e9a", basisOfRecord = "PRESERVED_SPECIMEN")
[1] 550849

Get possible values to be used in taxonomic rank arguments in functions

taxrank()
[1] "kingdom"       "phylum"        "class"         "order"        
[5] "family"        "genus"         "species"       "infraspecific"

Search for taxon information

Search for a genus

head(name_lookup(query = "Cnaemidophorus", rank = "genus", return = "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 125802004 1858636 125793784 Pterophoridae     <NA>       <NA> Insecta
4 131295800 1858636        NA          <NA>     <NA>       <NA>    <NA>
5 127882857 1858636 127804516 Pterophoridae Animalia Arthropoda Insecta
6 115123697 1858636        NA          <NA>     <NA>       <NA>    <NA>
        order        family          genus kingdomKey phylumKey  classKey
1 Lepidoptera Pterophoridae Cnaemidophorus  116630539 116762374 131743724
2 Lepidoptera Pterophoridae Cnaemidophorus          1        54       216
3 Lepidoptera Pterophoridae Cnaemidophorus         NA        NA 131714461
4        <NA>          <NA> Cnaemidophorus         NA        NA        NA
5 Lepidoptera Pterophoridae Cnaemidophorus  127795487 127795488 127795683
6        <NA>          <NA> 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 125810165 125793784 125802004 Cnaemidophorus Wallengren, 1862 WELLFORMED
4        NA        NA 131295800 Cnaemidophorus                  WELLFORMED
5 127795981 127804516 127882857 Cnaemidophorus                  WELLFORMED
6        NA        NA 115123697 Cnaemidophorus                  WELLFORMED
   rank numOccurrences
1 GENUS              0
2 GENUS              0
3 GENUS              0
4 GENUS              0
5 GENUS              0
6 GENUS              0

Search for the class mammalia

head(name_lookup(query = "mammalia")$data)
        key nubKey parentKey        parent   phylum         clazz
1 125798198    359 131712102      Chordata Chordata      Mammalia
2 116665331    359 116842680      Chordata Chordata      Mammalia
3       359    359        44      Chordata Chordata      Mammalia
4 125826646    359 131712102      Chordata Chordata      Mammalia
5 131754503    359 131754502 Macroscelidea Chordata Macroscelidea
6 102402290    359 102545028      Chordata Chordata      Mammalia
  phylumKey  classKey canonicalName     authorship   nameType  rank
1 131712102 125798198      Mammalia                WELLFORMED CLASS
2 116842680 116665331      Mammalia Linnaeus, 1758 WELLFORMED CLASS
3        44       359      Mammalia Linnaeus, 1758 WELLFORMED CLASS
4 131712102 125826646      Mammalia Linnaeus, 1758 WELLFORMED CLASS
5 116842680 131754502      Mammalia                WELLFORMED ORDER
6 102545028 102402290      Mammalia                WELLFORMED CLASS
  numOccurrences  kingdom kingdomKey    order  orderKey
1              0     <NA>         NA     <NA>        NA
2              0 Animalia  116630539     <NA>        NA
3              0 Animalia          1     <NA>        NA
4              0     <NA>         NA     <NA>        NA
5              0 Animalia  116630539 Mammalia 131754503
6              0 Animalia  101719444     <NA>        NA

Look up the species Helianthus annuus

head(name_lookup("Helianthus annuus", rank = "species")$data)
        key  nubKey parentKey     parent       kingdom     order
1 116845199 3119195 116853573 Helianthus       Plantae Asterales
2   3119195 3119195   3119134 Helianthus       Plantae Asterales
3 125790787 3119195 125809269 Helianthus          <NA> Asterales
4 106239436 3119195 106239325 Helianthus Viridiplantae Asterales
5 128399814 3119195 131338207 Helianthus          <NA>      <NA>
6 111449704 3119195 111449703 Helianthus       Plantae      <NA>
      family      genus kingdomKey  orderKey familyKey  genusKey
1 Asteraceae Helianthus  116668764 116852024 116856030 116853573
2 Asteraceae Helianthus          6       414      3065   3119134
3 Asteraceae Helianthus         NA 131717243 125799038 125809269
4 Asteraceae Helianthus  106147210 106237428 106237535 106239325
5       <NA> Helianthus         NA        NA        NA 131338207
6 Compositae Helianthus  111449174        NA 111442813 111449703
      canonicalName authorship   nameType    rank numOccurrences
1 Helianthus annuus         L. WELLFORMED SPECIES              0
2 Helianthus annuus         L. WELLFORMED SPECIES              0
3 Helianthus annuus         L. WELLFORMED SPECIES              0
4 Helianthus annuus            WELLFORMED SPECIES              0
5 Helianthus annuus            WELLFORMED SPECIES              0
6 Helianthus annuus         L. WELLFORMED SPECIES              0
         phylum         clazz phylumKey  classKey
1          <NA>          <NA>        NA        NA
2 Magnoliophyta Magnoliopsida        49       220
3          <NA>          <NA>        NA        NA
4  Streptophyta          <NA> 106171079        NA
5          <NA>          <NA>        NA        NA
6 Spermatophyta Dicotyledones 111449175 111449177

Get data for a single occurrence. Note that data is returned as a list, with slots for metadata and data, or as a hierarchy, or just data.

Just data

occ_get(key = 773433533, return = "data")
                  name       key longitude latitude
1 Helianthus annuus L. 773433533      -117    32.85

Just taxonomic hierarchy

occ_get(key = 773433533, return = "hier")
                  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

All data, or leave return parameter blank

occ_get(key = 773433533, return = "all")
$hierarch
                  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    32.85

Get many occurrences. occ_get is vectorized

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

Maps

Static map using the ggplot2 package

Make a map of Puma concolor occurrences

key <- name_backbone(name = "Puma concolor", kingdom = "plants")$speciesKey
dat <- occ_search(taxonKey = key, return = "data", limit = 300, minimal = FALSE)
gbifmap(input = dat)

plot of chunk gbifmap1