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In the ALA, all records are associated with an identifier that uniquely identifies the taxon to which that record belongs. However, taxonomic names are often ambiguous due to homonymy; i.e. re-use of names (common or scientific) in different clades. Hence, search_taxa provides a means to search for taxonomic names and check the results are 'correct' before proceeding to download data via atlas_occurrences(), atlas_species() or atlas_counts(). The resulting data.frame of taxonomic information can be passed to galah_identify() to provide the identify argument of atlas_ functions, which then filters the resulting records to the specified taxon or taxa.

Usage

search_taxa(...)

Arguments

...

: One or more scientific names, separated by commas and given as strings. If greater control is required to disambiguate search terms, taxonomic levels can be provided explicitly via a data.frame (see examples). 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.

Examples

Search using a single term

search_taxa("Reptilia")
#> # A tibble: 1 x 9
#>   search_term scientific_name taxon_concept_id                              rank  match_type kingdom  phylum  class  issues
#>   <chr>       <chr>           <chr>                                         <chr> <chr>      <chr>    <chr>   <chr>  <chr> 
#> 1 Reptilia    REPTILIA        urn:lsid:biodiversity.org.au:afd.taxon:682e1~ class exactMatch Animalia Chorda~ Repti~ noIss~

Note that search_taxa() is not case sensitive

search_taxa("reptilia") # not case sensitive
#> # A tibble: 1 x 9
#>   search_term scientific_name taxon_concept_id                              rank  match_type kingdom  phylum  class  issues
#>   <chr>       <chr>           <chr>                                         <chr> <chr>      <chr>    <chr>   <chr>  <chr> 
#> 1 reptilia    REPTILIA        urn:lsid:biodiversity.org.au:afd.taxon:682e1~ class exactMatch Animalia Chorda~ Repti~ noIss~

Search multiple taxa. search_taxa() will return one row per taxon

search_taxa(c("reptilia", "mammalia"))
#> # A tibble: 2 x 10
#>   search_term scientific_name taxon_concept_id                rank  match_type kingdom  phylum class issues vernacular_name
#>   <chr>       <chr>           <chr>                           <chr> <chr>      <chr>    <chr>  <chr> <chr>  <chr>          
#> 1 reptilia    REPTILIA        urn:lsid:biodiversity.org.au:a~ class exactMatch Animalia Chord~ Rept~ noIss~ <NA>           
#> 2 mammalia    MAMMALIA        urn:lsid:biodiversity.org.au:a~ class exactMatch Animalia Chord~ Mamm~ noIss~ Mammals

galah_identify() uses search_taxa() to narrow data queries

galah_call() |>
  galah_identify("reptilia") |>
  atlas_counts()
#> # A tibble: 1 x 1
#>     count
#>     <int>
#> 1 1317131

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.