Narrow a query by passing taxonomic identifiers

When conducting a search or creating a data query, it is common to identify a known taxon or group of taxa to narrow down the records or results returned.

Usage

galah_identify(..., search = NULL)

# S3 method for data_request
identify(x, ...)

# S3 method for metadata_request
identify(x, ...)

Arguments

...

One or more scientific names.

search

galah_identify() now always does a search to verify search terms; ergo this argument is ignored.

x

An object of class metadata_request, created using request_metadata()

Value

A tibble containing identified taxa.

Details

galah_identify() is used to identify taxa you want returned in a search or a data query. Users to pass scientific names or taxonomic identifiers with pipes to provide data only for the biological group of interest.

It is good to use search_taxa() and search_identifiers() first to check that the taxa you provide to galah_identify() return the correct results.

See also

search_taxa() to find identifiers from scientific names; search_identifiers() for how to get names if taxonomic identifiers are already known.

Examples

if (FALSE) {
# Specify a taxon. A valid taxon will return an identifier.
galah_identify("reptilia")

# Specify more than one taxon at a time.
galah_identify("reptilia", "mammalia", "aves", "pisces")

# Use `galah_identify()` to narrow your queries
galah_call() |> 
  galah_identify("Eolophus") |>
  atlas_counts()

# Within a pipe, `identify()` and `galah_identify()` are synonymous.
# hence the following is identical to the previous example:
request_data() |>
  identify("Eolophus") |>
  count() |>
  collect()

# If you know a valid taxon identifier, use `galah_filter()` instead.
# (This was formerly supported by `galah_identify()` with `search = FALSE`)
id <- "https://biodiversity.org.au/afd/taxa/009169a9-a916-40ee-866c-669ae0a21c5c"
galah_call() |> 
  galah_filter(lsid == id) |>
  atlas_counts()
}