search_all: Search for record information
In galah: Biodiversity Data from the GBIF Node Network

search_all

R Documentation

Search for record information

Description

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.

search_all() is a helper function that can do searches within multiple types of information from search_ sub-functions. See Details (below) for accepted values.

Usage

search_all(type, query)

search_assertions(query)

search_apis(query)

search_atlases(query)

search_collections(query)

search_datasets(query)

search_fields(query)

search_identifiers(...)

search_licences(query)

search_lists(query)

search_profiles(query)

search_providers(query)

search_ranks(query)

search_reasons(query)

search_taxa(...)

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.
`...`	A set of strings or a tibble to be queried

Details

There are five 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()`

Value

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

References

Darwin Core terms https://dwc.tdwg.org/terms/

Examples

## Not run: 
# 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))

## End(Not run)

galah documentation built on Nov. 20, 2023, 9:07 a.m.