The GBIF network consists of a series of a series of ‘node’
organisations who collate biodiversity data from their own countries,
with GBIF acting as an umbrella organisation to store data from all
nodes. Several nodes have their own APIs, often built from the ‘living
atlas’ codebase developed by the ALA. At present, galah
supports the following functions and atlases:
Set which atlas you want to use by changing the atlas
argument in galah_config(). The atlas argument
can accept a full name, an acronym, or a region to select a given atlas,
all of which are available via show_all(atlases). Once a
value is provided, it will automatically update galah’s
server configuration to your selected atlas. The default
atlas is Australia.
If you intend to download records, you may need to register a user profile with the relevant atlas first.
galah_config(atlas = "GBIF.es", email = "your_email_here")You can use the same look-up functions to find useful information about the Atlas you have set. Available information may vary for each Living Atlas.
galah_config(atlas = "Guatemala")## Atlas selected: Sistema Nacional de Información sobre Diversidad Biológica de Guatemala (SNIBgt) [Guatemala]show_all(datasets)## # A tibble: 100 × 3
## name uri uid
## <chr> <chr> <chr>
## 1 A Distribution and Taxonomic Reference Dataset of Geranium (Geraniaceae) in the New World http… dr321
## 2 A global database for the distributions of crop wild relatives http… dr12
## 3 A matrix-based revision of the genus Hypogena Dejean, 1834 (Coleoptera Tenebrionidae) http… dr467
## 4 A new Mexican species of Chrysina Kirby (Coleoptera: Scarabaeidae: Rutelinae), with nomenclatural changes, new re… http… dr554
## 5 A new species of Setostylus Matile and new records of Setostylus bellulus (Williston) (Diptera: Keroplatidae) http… dr538
## 6 A revision of the genus Bromeloecia Spuler (Diptera: Sphaeroceridae: Limosininae) http… dr481
## 7 A synopsis of American Caraphia Gahan, 1906 (Coleoptera: Cerambycidae: Lepturinae) with description of two new sp… http… dr539
## 8 A synopsis of the Neotropical genus Protoneura (Odonata: Coenagrionidae) http… dr448
## 9 A systematic revision of the genus Archocentrus (Perciformes: Cichlidae), with the description of two new genera … http… dr362
## 10 A taxonomic monograph of the genus Tylodinus Champion (Coleoptera: Curculionidae: Cryptorhynchinae: Tylodina) of … http… dr564
## # … with 90 more rowsshow_all(fields)## # A tibble: 129 × 4
## id description type link
## <chr> <chr> <chr> <chr>
## 1 all_image_url Image URLs for this record fiel… <NA>
## 2 assertion_user_id User ID of the person who has made an assertion about this record fiel… <NA>
## 3 assertions A list of all assertions (user and system supplied) for a record resulting from data quality… fiel… <NA>
## 4 assertions_missing Assertion indicating missing field values for a record. E.g. missing basis of record fiel… <NA>
## 5 assertions_passed Assertion indicating a data quality test has been passed by this record fiel… <NA>
## 6 assertions_unchecked Assertion indicating a data quality test was not performed for this record typically due to … fiel… <NA>
## 7 basis_of_record The basis of record e.g. Specimen, Observation http://rs.tdwg.org/dwc/terms/basisOfRecord fiel… <NA>
## 8 catalogue_number http://rs.tdwg.org/dwc/terms/catalogNumber fiel… <NA>
## 9 class The class the Atlas has matched this record to in the NSL http://rs.tdwg.org/dwc/terms/class fiel… <NA>
## 10 collection_code The collection code for this record. This will be populated if the data has come from a muse… fiel… <NA>
## # … with 119 more rowssearch_all(fields, "year")## # A tibble: 3 × 4
## id description type link
## <chr> <chr> <chr> <chr>
## 1 year http://rs.tdwg.org/dwc/terms/year fiel… <NA>
## 2 occurrence_year Year ranges for a search. Calculated based on the unique values for a query. fiel… <NA>
## 3 date_precision The precision of the date information for the record. Values include 'Day', 'Month', 'Year', 'Year… fiel… <NA>search_taxa("lagomorpha")## # A tibble: 1 × 12
## search_term taxon_concept_id scientific_name scientific_name_authorship rank kingdom phylum class order family genus species
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 lagomorpha 785 Lagomorpha <NA> order Animalia Chorda… Mamm… Lago… <NA> <NA> <NA>You can build queries as you normally would in galah.
For taxonomic queries, use search_taxa() to make sure your
searches are returning the correct taxonomic data.
galah_config(atlas = "United Kingdom")## Atlas selected: National Biodiversity Network (NBN) [United Kingdom]search_taxa("vlps") # Returns no data due to misspelling## # A tibble: 1 × 1
## search_term
## <chr>
## 1 vlpssearch_taxa("vulpes") # Returns data## # A tibble: 1 × 13
## search_term taxon_concept_id scientific_name scientific_name_au…¹ rank kingdom super…² order class genus phylum family species
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 vulpes NBNSYS0000138878 Vulpes Frisch, 1775 genus Animal… Tetrap… Carn… Mamm… Vulp… Chord… Canid… <NA>
## # … with abbreviated variable names ¹scientific_name_authorship, ²superclassgalah_call() |>
galah_identify("vulpes") |>
galah_filter(year > 2010) |>
atlas_counts()## # A tibble: 1 × 1
## count
## <int>
## 1 98000Download species occurrence records from other atlases with
atlas_occurrences()
galah_config(atlas = "Guatemala")## Atlas selected: Sistema Nacional de Información sobre Diversidad Biológica de Guatemala (SNIBgt) [Guatemala]galah_call() |>
galah_identify("Lagomorpha") |>
galah_filter(year <= 1980) |>
galah_select(taxon_name, year) |>
atlas_occurrences()## # A tibble: 39 × 2
## scientificName year
## <chr> <dbl>
## 1 Sylvilagus floridanus (J. A. Allen, 1890) 1968
## 2 Sylvilagus brasiliensis subsp. truei (J. Allen, 1890) 1947
## 3 Sylvilagus floridanus (J. A. Allen, 1890) 1968
## 4 Sylvilagus floridanus (J. A. Allen, 1890) 1968
## 5 Sylvilagus floridanus subsp. aztecus (J. Allen, 1890) 1924
## 6 Sylvilagus floridanus subsp. aztecus (J. Allen, 1890) 1924
## 7 Sylvilagus floridanus (J. A. Allen, 1890) 1906
## 8 Sylvilagus floridanus (J. A. Allen, 1890) 1906
## 9 Sylvilagus floridanus (J. A. Allen, 1890) 1960
## 10 Sylvilagus brasiliensis subsp. truei (J. Allen, 1890) 1960
## # … with 29 more rowsIt is also possible to create more complex queries that return data
from multiple Living Atlases. As an example, setting atlases within a
loop with galah_config() and purrr::map()
allows us to return the total number of species records in each Living
Atlas in one table.
library(purrr)
library(tibble)
library(dplyr)
library(gt)
atlases <- show_all(atlases)
counts <- map(atlases$region,
function(x){
galah_config(atlas = x)
atlas_counts()
})
tibble(
atlas = atlases$region,
n = unlist(counts)) |>
filter(n > 0) |>
arrange(desc(n)) |>
gt() |>
fmt_number(column = n)| atlas | n |
|---|---|
| Global | 1,803,221,416.00 |
| United Kingdom | 207,672,900.00 |
| France | 128,490,040.00 |
| Australia | 112,998,157.00 |
| Sweden | 103,417,222.00 |
| Spain | 38,279,454.00 |
| Brazil | 23,739,468.00 |
| Portugal | 16,043,865.00 |
| Austria | 8,075,385.00 |
| Estonia | 7,127,695.00 |
| Guatemala | 3,586,634.00 |