International Atlases

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()

Set Atlas

Use ala_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.

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

Get data for another atlas

ala_counts()

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)
ala_counts(taxa = id)

Retrieving occurrence records

# Download records from the Austrian atlas
ala_config(atlas = "Austria")
id <- get_gbifid("bombina variegata", rows = 1)
ala_counts(taxa = id)
occ <- read.csv('bombina_variegata.csv')
occ <- ala_occurrences(taxa = id)
head(occ)

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.



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galah documentation built on July 2, 2021, 9:07 a.m.