The Global Biodiversity Information Facility (GBIF; https://www.gbif.org)
provides tools to enable users to find, access, combine and visualise
biodiversity data. galah
enables the R community to directly access data and
resources hosted by GBIF and several of it's subsidiary organisations, known
as 'nodes'. The basic unit of observation stored by these infrastructures 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, or 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.
For those outside Australia, 'galah' is the common name of Eolophus roseicapilla, a widely-distributed Australian bird species.
Functions
Piping functions
galah_call()
orrequest_()
et al. Start to build a data querycollapse()
Generate a querycompute()
Compute a querycollect()
Retrieve a database query
Lazy data manipulation
identify()
orgalah_identify()
Search for taxonomic identifiersfilter()
orgalah_filter()
Filter recordsselect()
orgalah_select()
Fields to report information forgroup_by()
orgalah_group_by()
Fields to group counts byst_crop()
orgalah_geolocate()
Specify a locationapply_profile()
orgalah_apply_profile()
Restrict to data that pass predefined checks (ALA only)slice_head()
Choose the first n rows of a downloadarrange()
Arrange rows of a query on the server side
Download data
atlas_occurrences()
Download occurrence recordsatlas_counts()
orcount()
Count the number of records or species returned by a queryatlas_species()
Download species listsatlas_taxonomy()
Return a section of the ALA taxonomic treeatlas_media()
View images and sounds available to downloadcollect_media()
Download images and sounds
Look up information
search_taxa()
Search for taxa using a text-searchsearch_identifiers()
Search for taxa using taxonomic identifiersshow_all()
&search_all()
Data for generating filter queriesshow_values()
&search_values()
Show or search for values withinfields
,profiles
,lists
,collections
,datasets
orproviders
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. The easiest way to do this
is to start a pipe with galah_call()
and follow it with the relevant
dplyr
function; starting with filter()
, but also including select()
,
group_by()
or others. Functions without a relevant dplyr
synonym include
galah_identify()
/identify()
for choosing a taxon, or galah_geolocate()
/
st_crop()
for choosing a specific location. 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).
Author
Maintainer: Martin Westgate martin.westgate@csiro.au
Authors:
Matilda Stevenson
Dax Kellie dax.kellie@csiro.au
Peggy Newman peggy.newman@csiro.au