Look up taxon information

Look up taxonomic names before downloading data from the ALA, using atlas_occurrences(), atlas_species() or atlas_counts(). Taxon information returned by search_taxa() may be passed to galah_identify() to provide the identify argument of atlas_ functions. search_taxa() allows users to disambiguate homonyms (i.e. where the same name refers to taxa in different clades) prior to downloading data.

Usage

search_taxa(...)

Arguments

...

: A string of one or more scientific names, separated by commas, or a data frame specifying taxonomic levels. Note that searches are not case-sensitive.

Value

An object of class tbl_df, data.frame (aka a tibble) and ala_id

containing taxonomic information.

Details

Users can also specify taxonomic levels in a search using a data frame (tibble). Taxa may be specified using either the specificEpithet argument to designate the second element of a Latin binomial, or the scientificName argument to specify the scientific name (which may include the subspecific epithet if required).

See also

search_identifiers() for how to get names if taxonomic identifiers are already known. galah_identify(), galah_select(), galah_filter(), and galah_geolocate() for ways to restrict the information returned by atlas_occurrences() and related functions. atlas_taxonomy() to look up taxonomic trees.

Examples

if (FALSE) {
# Search using a single string. 
# Note that `search_taxa()` isn't case sensitive
search_taxa("Reptilia")

# Search using multiple strings. 
# `search_taxa()` will return one row per taxon
search_taxa("reptilia", "mammalia")

# Specify taxonomic levels in a tibble using "specificEpiphet"
search_taxa(tibble::tibble(
  class = "aves", 
  family = "pardalotidae", 
  genus = "pardalotus", 
  specificEpithet = "punctatus"))

# Specify taxonomic levels in a tibble using "scientificName"                    
search_taxa(tibble::tibble(
  family = c("pardalotidae", "maluridae"), 
  scientificName = c("Pardalotus striatus striatus", "malurus cyaneus")))

# `galah_identify()` uses `search_taxa()` to narrow data queries
taxa <- search_taxa("reptilia", "mammalia")
galah_call() |>
  galah_identify(taxa) |>
  atlas_counts()
}