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The architecture developed by the ALA to store biodiversity data is used by over 20 International Living Atlases. Although there are slight differences in the core components of each Atlas’s architecture, galah is flexible enough to handle most of these differences. As a result, it is possible to change which Living Atlas you get data from in galah

Supported Atlases

To see which international Living Atlases galah currently supports, use
show_all_atlases().

## # A tibble: 10 × 4
##    atlas          institution                                                             acronym url                         
##    <chr>          <chr>                                                                   <chr>   <chr>                       
##  1 Australia      Atlas of Living Australia                                               ALA     https://www.ala.org.au      
##  2 Austria        Biodiversitäts-Atlas Österreich                                         BAO     https://biodiversityatlas.at
##  3 Brazil         Sistemas de Informações sobre a Biodiversidade Brasileira               SiBBr   https://sibbr.gov.br        
##  4 Estonia        eElurikkus                                                              <NA>    https://elurikkus.ee        
##  5 France         Inventaire National du Patrimoine Naturel                               INPN    https://inpn.mnhn.fr        
##  6 Guatemala      Sistema Nacional de Información sobre Diversidad Biológica de Guatemala SNIBgt  https://snib.conap.gob.gt   
##  7 Portugal       GBIF Portugal                                                           GBIF.pt https://www.gbif.pt         
##  8 Spain          GBIF Spain                                                              GBIF.es https://www.gbif.es         
##  9 Sweden         Swedish Biodiversity Data Infrastructure                                SBDI    https://biodiversitydata.se 
## 10 United Kingdom National Biodiversity Network                                           NBN     https://nbn.org.uk

Some atlases support more types of data queries than others (e.g. counts, occurrences, species lists). To see what kinds of information and data can be returned from each atlase, you can see the list of supported Application Programming Interfaces (APIs).

show_all(apis)
## # A tibble: 167 × 5
##    atlas     system       api_name                api_url                                                                     calle…¹
##    <chr>     <chr>        <chr>                   <chr>                                                                       <chr>  
##  1 Australia collections  collections_collections https://collections.ala.org.au/ws/collection                                show_a…
##  2 Australia collections  collections_datasets    https://collections.ala.org.au/ws/dataResource                              show_a…
##  3 Australia collections  collections_providers   https://collections.ala.org.au/ws/dataProvider                              show_a…
##  4 Australia data-quality profiles_all            https://data-quality-service.ala.org.au/api/v1/data-profiles                show_a…
##  5 Australia data-quality profiles_lookup         https://data-quality-service.ala.org.au/api/v1/quality/activeProfile?profi… show_p…
##  6 Australia doi          doi_download            https://apis.ala.org.au/doi/api/doi/{doi_string}/download                   doi_do…
##  7 Australia images       image_licences          https://images.ala.org.au/ws/licence                                        show_a…
##  8 Australia images       image_metadata          https://images.ala.org.au/ws/image/{id}                                     media_…
##  9 Australia lists        lists_all               https://lists.ala.org.au/ws/speciesList                                     show_a…
## 10 Australia lists        lists_lookup            https://lists.ala.org.au/ws/speciesListItems/{list_id}                      show_l…
## # … with 157 more rows, and abbreviated variable name ¹​called_by

Set Atlas

Set which atlas you want to use by changing the atlas argument in galah_config(). This 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 = "Spain", 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")

show_all(datasets)
## # A tibble: 522 × 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 record… 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 species 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 and … http… dr362
## 10 A taxonomic monograph of the genus Tylodinus Champion (Coleoptera: Curculionidae: Cryptorhynchinae: Tylodina) of Chia… http… dr564
## # … with 512 more rows
show_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 tes… 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 the … 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 museum o… fiel… <NA> 
## # … with 119 more rows
search_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 ran… 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 Chordata Mammalia Lago… <NA>   <NA>  <NA>

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")

search_taxa("vlps")   # Returns no data due to misspelling
## # A tibble: 1 × 1
##   search_term
##   <chr>      
## 1 vlps
search_taxa("vulpes") # Returns data
## # A tibble: 1 × 13
##   search_term taxon_concept_id scientific_name scientific_name_author…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 ¹​scientific_name_authorship, ²​superclass
galah_call() |>
  galah_identify("vulpes") |>
  galah_filter(year > 2010) |>
  atlas_counts()
## # A tibble: 1 × 1
##   count
##   <int>
## 1 97224

Download species occurrence records from other atlases with atlas_occurrences()

galah_config(atlas = "Guatemala")

galah_call() |>
  galah_identify("Lagomorpha") |>
  galah_filter(year <= 1980) |>
  galah_select(taxon_name, year) |>
  atlas_occurrences()
## # A tibble: 39 × 2
##    scientificName                                         year
##    <chr>                                                 <int>
##  1 Sylvilagus floridanus (J. A. Allen, 1890)              1968
##  2 Sylvilagus floridanus (J. A. Allen, 1890)              1906
##  3 Sylvilagus brasiliensis subsp. truei (J. Allen, 1890)  1947
##  4 Sylvilagus floridanus (J. A. Allen, 1890)              1968
##  5 Sylvilagus floridanus (J. A. Allen, 1890)              1968
##  6 Sylvilagus floridanus (J. A. Allen, 1890)              1906
##  7 Sylvilagus floridanus (J. A. Allen, 1890)              1960
##  8 Sylvilagus brasiliensis subsp. truei (J. Allen, 1890)  1960
##  9 Sylvilagus floridanus (J. A. Allen, 1890)              1952
## 10 Sylvilagus floridanus (J. A. Allen, 1890)              1955
## # … with 29 more rows

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$atlas, 
  function(x){
    galah_config(atlas = x)
    atlas_counts()
})

tibble(
  atlas = atlases$atlas, 
  n = unlist(counts)) |> 
  filter(n > 0) |>
  arrange(desc(n)) |>
  gt()
atlas n
United Kingdom 205571136
Australia 114080945
Sweden 103417222
France 87443384
Spain 38269601
Brazil 23316770
Portugal 16043865
Austria 7813712
Estonia 6972683
Guatemala 3509690