
Choosing an atlas
Martin Westgate, Dax Kellie
2023-11-07
Source:vignettes/choosing_an_atlas.Rmd
choosing_an_atlas.Rmd
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 Organisation
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")
Look up Information
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
Download data
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
Complex queries with multiple Atlases
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 |