Search for record information

The living atlases store a huge amount of information, above and beyond the occurrence records that are their main output. In galah, one way that users can investigate this information is by searching for a specific option or category for the type of information they are interested in. Functions prefixed with search_ do this, displaying any matches to a search term within the valid options for the information specified by the suffix.

For more information about taxonomic searches using search_taxa(), see ?taxonomic_searches.

search_all() is a helper function that can do searches for multiple types of information, acting as a wrapper around many search_ sub-functions. See Details (below) for accepted values.

Usage

search_all(type, query, all_fields = FALSE)

search_assertions(query, all_fields = FALSE)

search_apis(query, all_fields = FALSE)

search_atlases(query, all_fields = FALSE)

search_collections(query, all_fields = FALSE)

search_datasets(query, all_fields = FALSE)

search_fields(query, all_fields = FALSE)

search_identifiers(..., all_fields = FALSE)

search_licences(query, all_fields = FALSE)

search_lists(query, all_fields = FALSE)

search_media(query, all_fields = FALSE)

search_profiles(query, all_fields = FALSE)

search_providers(query, all_fields = FALSE)

search_ranks(query, all_fields = FALSE)

search_reasons(query, all_fields = FALSE)

search_taxa(..., all_fields = FALSE)

Arguments

type

A string to specify what type of parameters should be searched.

query

A string specifying a search term. Searches are not case-sensitive.

all_fields

If TRUE, show_values() also returns all columns available from the API, rather than the 'default' columns traditionally provided via galah.

...

One or more objects accepted by the taxonomic lookup services. See taxonomic_searches for details

Value

An object of class tbl_df and data.frame (aka a tibble) containing all data that match the search query.

Details

There are six categories of information, each with their own specific sub-functions to look-up each type of information. The available types of information for search_all() are:

Category	Type	Description	Sub-functions
configuration	atlases	Search for what atlases are available	search_atlases()
	apis	Search for what APIs & functions are available for each atlas	search_apis()
	reasons	Search for what values are acceptable as 'download reasons' for a specified atlas	search_reasons()
taxonomy	taxa	Search for one or more taxonomic names	search_taxa()
	identifiers	Take a universal identifier and return taxonomic information	search_identifiers()
	ranks	Search for valid taxonomic ranks (e.g. Kingdom, Class, Order, etc.)	search_ranks()
filters	fields	Search for fields that are stored in an atlas	search_fields()
	assertions	Search for results of data quality checks run by each atlas	search_assertions()
	licenses	Search for copyright licences applied to media	search_licenses()
group filters	profiles	Search for what data profiles are available	search_profiles()
	lists	Search for what species lists are available	search_lists()
data providers	providers	Search for which institutions have provided data	search_providers()
	collections	Search for the specific collections within those institutions	search_collections()
	datasets	Search for the data groupings within those collections	search_datasets()
media	media	Search for images or sounds using a vector of IDs	search_media()

See also

Use the show_all() function and show_all_() sub-functions to show available options of information. These functions are used to pass valid arguments to filter(), select(), and related functions. Taxonomic queries are somewhat more involved; see taxonomic_searches for details.

Examples

if (FALSE) { # \dontrun{
# Search for fields that include the word "date"
search_all(fields, "date")

# Search for fields that include the word "marine"
search_all(fields, "marine")

# Search using a single taxonomic term
# (see `?search_taxa()` for more information)
search_all(taxa, "Reptilia") # equivalent

# Look up a unique taxon identifier
# (see `?search_identifiers()` for more information)
search_all(identifiers, 
           "https://id.biodiversity.org.au/node/apni/2914510")

# Search for species lists that match "endangered"
search_all(lists, "endangered") # equivalent

# Search for a valid taxonomic rank, "subphylum"
search_all(ranks, "subphylum")

# An alternative is to download the data and then `filter` it. This is 
# largely synonymous, and allows greater control over which fields are searched.
request_metadata(type = "fields") |>
 collect() |>
 dplyr::filter(grepl("date", id))
} # }