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.
search_taxa(...): 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.
An object of class tbl_df, data.frame (aka a tibble) and ala_id
containing taxonomic information.
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
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.