Biodiversity Data from the Living Atlas Community

The living atlas community provides tools to enable users to find, access, combine and visualise data on biodiversity. 'galah' enables the R community to directly access data and resources hosted by the living atlases. The basic unit of observation is an occurrence record, based on the 'Darwin Core' data standard (https://dwc.tdwg.org); however galah also enables users to locate and download taxonomic information, associated media such images or sounds, all while restricting their queries to particular taxa or locations. Users can specify which columns are returned by a query, or restrict their results to observations that meet particular quality-control criteria.

Functions

Start a data query

galah_call() Start to build a data query

Narrow your results

galah_identify() or identify() Search for taxonomic identifiers
galah_filter() or filter() Filter records
galah_select() or select() Fields to report information for
galah_group_by() or group_by() Fields to group counts by
galah_geolocate() or st_crop() Specify a location
galah_apply_profile() Restrict to data that pass predefined checks (ALA only)
galah_down_to() Specify a taxonomic rank
slice_head() Choose the first n rows of a download

Download data

atlas_occurrences() Download occurrence records
atlas_counts() or count() Count the number of records or species returned by a query
atlas_species() Download species lists
atlas_taxonomy() Return a section of the ALA taxonomic tree
atlas_media() View images and sounds available to download
collect_media() Download images and sounds
collect_occurrences() Download previously-defined sets of occurrence records

Look up information

search_taxa() Search for taxa using a text-search
search_identifiers() Search for taxa using taxonomic identifiers
show_all() & search_all() Data for generating filter queries
show_values() & search_values() Show or search for values within fields, profiles, lists, collections, datasets or providers

Manage cache

show_all_cached_files() List previously cached files and their metadata
clear_cached_files() Clear previously cached files and their metadata

Configure session

galah_config() Package configuration options

Cite

atlas_citation() Citation for a dataset

Terminology

To get the most value from galah, it is helpful to understand some terminology. Each occurrence record contains taxonomic information, and usually some information about the observation itself, such as its location. In addition to this record-specific information, the living atlases append contextual information to each record, particularly data from spatial layers reflecting climate gradients or political boundaries. They also run a number of quality checks against each record, resulting in assertions attached to the record. Each piece of information associated with a given occurrence record is stored in a field, which corresponds to a column when imported to an R data.frame. See show_all(fields) to view valid fields, layers and assertions, or conduct a search using search_all(fields).

Data fields are important because they provide a means to filter occurrence records; i.e. to return only the information that you need, and no more. Consequently, much of the architecture of galah has been designed to make filtering as simple as possible. Functions with the galah_ prefix offer ways to shape your query call. Each galah_ function allows the user to filter in a different way. Again, the function suffix reveals what each one does. galah_filter(), galah_select() and galah_group_by() intentionally match dplyr's select(), filter() and group_by() functions, both in their name and how they they are used. For example, you can use galah_select() to choose what information is returned as columns. Alternatively, you can use galah_filter() to filter the rows. You can also choose specific taxa with galah_identify() or choose a specific location using galah_geolocate(). By combining different filters, it is possible to build complex queries to return only the most valuable information for a given problem.

A notable extension of the filtering approach is to remove records with low 'quality'. All living atlases perform quality control checks on all records that they store. These checks are used to generate new fields, that can then be used to filter out records that are unsuitable for particular applications. However, there are many possible data quality checks, and it is not always clear which are most appropriate in a given instance. Therefore, galah supports data quality profiles, which can be passed to galah_apply_profile() to quickly remove undesirable records. A full list of data quality profiles is returned by show_all(profiles). Note this service is currently only available for the Australian atlas (ALA).

For those outside Australia, 'galah' is the common name of Eolophus roseicapilla, a widely-distributed Australian bird species.

Package design

In most cases, users will be primarily interested in using galah to return data from one of the living atlases. These functions are named with the prefix atlas_, followed by a suffix describing the information that they provide. For example, users that wish to download occurrence data can use the function atlas_occurrences(). Alternatively, users that wish to download data on each species (rather than on each occurrence record) can use atlas_species() or download media content (largely images) using atlas_media(). Users can also assess how many records meet their particular criteria using atlas_counts() and return a taxonomic tree for a specific clade from one level down to another level (e.g., from family to genus). All functions return a data.frame as their standard format, except atlas_taxonomy() which returns a data.tree.

Functions in galah are designed according to a nested architecture. Users that require data should begin by locating the relevant atlas_ function; the arguments within that function then call correspondingly-named galah_ functions; specific values that can be interpreted by those galah_ functions can be searched for or listed using search_all() and show_all() functions; desired taxa can be also be identified using search_taxa() and passed within galah_identify() to the taxa argument of atlas_ functions.

References

For more information on the ALA API, visit https://docs.ala.org.au/. If you have any questions, comments or suggestions, please email support@ala.org.au.

Author

Maintainer: Martin Westgate martin.westgate@csiro.au

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