International Atlases

Matilda Stevenson

2021-08-05

The software developed by the ALA is now used by 27 International Living Atlases. Although there are differences in the versions of core components used by the Atlases, and variations in the web services available, galah is flexible enough to handle most of these differences. Below we explain how to change the Living Atlas the package points to, and how to put in a pull request if you would like to see another Living Atlas supported in galah.

Supported Atlases

To show the Atlases currently supported by galah, use find_atlases(). This function also provides information on which taxonomic source each Atlas uses.

library(galah)
find_atlases()
##       atlas taxonomy_source                                                     taxonomy_info
## 1 Australia             ALA                                           https://bie.ala.org.au/
## 2   Austria            GBIF https://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c
## 3 Guatemala            GBIF https://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c
## 4     Spain            GBIF https://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c
## 5    Sweden            GBIF https://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c
## 6        UK             NBN            https://www.nhm.ac.uk/our-science/data/uk-species.html

Set Atlas

Use galah_config() to set the Atlas to use. This will automatically populate the server configuration for your selected Atlas. By default, the atlas is Australia. If you intend to download records you will need to register with the relevant Atlas.

galah_config(atlas = "UK", email = "your_email_here")

Get data for another atlas

ala_counts()
## [1] 200068504

Using taxonomic filters for another atlas

galah only supports searching for Australian taxonomy; for other Atlases, taxize should be used to search for the taxonomic id, and this id can be passed to the taxa argument of ala_ functions. For example:

library(taxize)
# Use UK taxonomy
id <- get_nbnid("Vulpes vulpes", rows = 1)
## ==  1 queries  ===============
## 
## Retrieving data for taxon 'Vulpes vulpes'
## v  Found:  Vulpes vulpes
## ==  Results  =================
## 
## * Total: 1 
## * Found: 1 
## * Not Found: 0
ala_counts(taxa = id)
## [1] 149388

Retrieving occurrence records

# Download records from the Austrian atlas
galah_config(atlas = "Austria")
id <- get_gbifid("bombina variegata", rows = 1)
## ==  1 queries  ===============
## 
## Retrieving data for taxon 'bombina variegata'
## v  Found:  bombina variegata
## ==  Results  =================
## 
## * Total: 1 
## * Found: 1 
## * Not Found: 0
ala_counts(taxa = id)
## [1] 392
occ <- ala_occurrences(taxa = id)
head(occ)
##   X decimalLatitude decimalLongitude  eventDate    scientificName taxonConceptID                             recordID
## 1 1        47.04326         15.15363 2021-03-31 Bombina variegata        2423435 a358fdd5-500f-4963-9454-545a88172748
## 2 2        46.65526         15.52156 2014-03-27 Bombina variegata        2423435 9212accb-b19e-465c-85b2-df6f018e83ef
## 3 3        48.12541         16.05689            Bombina variegata        2423435 e331e44e-fcc2-4da2-ac4a-9a2f6265530c
## 4 4        48.12321         16.05636            Bombina variegata        2423435 da843bec-ab22-4719-b268-b26c89835749
## 5 5        48.12044         16.05967            Bombina variegata        2423435 b2db97ae-d8ac-413c-be20-eed1aa485a32
## 6 6        48.45346         15.37861            Bombina variegata        2423435 b140bb0e-b7af-4fdc-9f9e-510980a73e09

Supporting another Atlas

galah currently supports a subset of the existing Living Atlases. If you would like to see another Living Atlas supported, add the server configuration for the Atlas in the R/find_atlases.R file, and put in a pull request.