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: 1,283 × 3 ## id name uri ## <chr> <chr> <chr> ## 1 dr1440 A catalogue of the Heteroptera (Hemiptera) or true bugs of Argentina http… ## 2 dr1436 A cybercatalogue of American sand fly types (Diptera, Psychodidae, Phleboto… http… ## 3 dr1226 A distinctive new species of biting midge in the subgenus Euprojoannisia Br… http… ## 4 dr321 A Distribution and Taxonomic Reference Dataset of Geranium (Geraniaceae) in… http… ## 5 dr1285 A geographic distribution database of the cassava whitefly complex (Hemipte… http… ## 6 dr12 A global database for the distributions of crop wild relatives http… ## 7 dr467 A matrix-based revision of the genus Hypogena Dejean, 1834 (Coleoptera Tene… http… ## 8 dr1061 A Monographic Revision of the Genus Hoplopyga Thomson, 1880 (Coleoptera: Sc… http… ## 9 dr1570 A new Anomiopus Westwood (Coleoptera: Scarabaeidae: Scarabaeinae) from the … http… ## 10 dr1177 A new Central American genus of pleasing fungus beetles (Coleoptera: Erotyl… http… ## # ℹ 1,273 more rows
show_all(fields)
## # A tibble: 128 × 3 ## id description type ## <chr> <chr> <chr> ## 1 all_image_url <NA> fields ## 2 assertion_user_id Assertions by user fields ## 3 assertions Record issues fields ## 4 assertions_missing <NA> fields ## 5 assertions_passed <NA> fields ## 6 assertions_unchecked <NA> fields ## 7 basis_of_record Record type fields ## 8 catalogue_number Catalogue Number fields ## 9 cl10011 <NA> fields ## 10 class Class fields ## # ℹ 118 more rows
search_all(fields, "year")
## # A tibble: 2 × 3 ## id description type ## <chr> <chr> <chr> ## 1 year Year fields ## 2 occurrence_year Date (by decade) fields
search_taxa("lagomorpha")
## # A tibble: 1 × 8 ## search_term scientific_name taxon_concept_id rank kingdom phylum class order ## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> ## 1 lagomorpha Lagomorpha 785 order Animalia Chordata Mammalia Lagomorpha
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: 0 × 0
search_taxa("vulpes") # Returns data
## # A tibble: 1 × 12 ## search_term scientific_name scientific_name_author…¹ taxon_concept_id rank kingdom phylum ## <chr> <chr> <chr> <chr> <chr> <chr> <chr> ## 1 vulpes Vulpes Frisch, 1775 NBNSYS0000138878 genus Animal… Chord… ## # ℹ abbreviated name: ¹scientific_name_authorship ## # ℹ 5 more variables: class <chr>, order <chr>, family <chr>, genus <chr>, superclass <chr>
galah_call() |> galah_identify("vulpes") |> galah_filter(year > 2010) |> atlas_counts()
## # A tibble: 1 × 1 ## count ## <int> ## 1 123736
Download 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: 4 × 2 ## scientificName year ## <chr> <dbl> ## 1 Erinnyis ello subsp. ello 1973 ## 2 Aellopos titan Burmeister, 1856 1971 ## 3 Manduca rustica Fabricius, 1775 1930 ## 4 Manduca rustica Fabricius, 1775 1930
It 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() }) atlases |> select(region, institution) |> bind_cols(bind_rows(counts)) |> arrange(desc(count)) |> gt() |> fmt_number(column = count)
region | institution | count |
---|---|---|
Global | Global Biodiversity Information Facility | 2,083,165,001.00 |
United Kingdom | National Biodiversity Network | 254,155,214.00 |
France | Portail français d'accès aux données d'observation sur les espèces | 143,668,494.00 |
Australia | Atlas of Living Australia | 131,963,195.00 |
Sweden | Swedish Biodiversity Data Infrastructure | 124,556,849.00 |
Spain | GBIF Spain | 57,696,934.00 |
Brazil | Sistemas de Informações sobre a Biodiversidade Brasileira | 24,369,137.00 |
Portugal | GBIF Portugal | 16,043,865.00 |
Austria | Biodiversitäts-Atlas Österreich | 8,976,175.00 |
Estonia | eElurikkus | 7,475,447.00 |
Guatemala | Sistema Nacional de Información sobre Diversidad Biológica de Guatemala | 3,617,694.00 |
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