The ALA has its' own internal taxonomy that is derived from authoritative
sources. atlas_taxonomy provides a means to query
that taxonomy, returning a tree (class Node) showing which lower
clades are contained within the specified taxon.
atlas_taxonomy(request = NULL, identify = NULL, down_to = NULL)optional data_rquest object: generated by a call to
galah_call().
data.frame: generated by a call to
galah_identify().
The identity of the clade at which the downwards search
should stop. Should be specified using an object of class
character and galah_down_to, as returned from
galah_down_to(). Also accepts a string.
A tree consisting of objects of class Node, containing the
requested taxonomy. Each node contains the following attributes:
name: The scientific name of the taxon in question
rank: The taxonomic rank to which that taxon belongs
guid: A unique identifier used by the ALA
authority: The source of the taxonomic name & identifier
Get a taxonomic tree of Chordata down to the class level
galah_call() |>
galah_identify("chordata") |>
galah_down_to(class) |>
atlas_taxonomy()
#> levelName
#> 1 Chordata
#> 2 <U+00A6>--Cephalochordata
#> 3 <U+00A6> <U+00B0>--Amphioxi
#> 4 <U+00A6>--Craniata
#> 5 <U+00A6> <U+00B0>--Agnatha
#> 6 <U+00A6> <U+00A6>--Cephalasipidomorphi
#> 7 <U+00A6> <U+00B0>--Myxini
#> 8 <U+00A6>--Tunicata
#> 9 <U+00A6> <U+00A6>--Appendicularia
#> 10 <U+00A6> <U+00A6>--Ascidiacea
#> 11 <U+00A6> <U+00B0>--Thaliacea
#> 12 <U+00B0>--Vertebrata
#> 13 <U+00B0>--Gnathostomata
#> 14 <U+00A6>--Amphibia
#> 15 <U+00A6>--Aves
#> 16 <U+00A6>--Mammalia
#> 17 <U+00A6>--Pisces
#> 18 <U+00A6> <U+00A6>--Actinopterygii
#> 19 <U+00A6> <U+00A6>--Chondrichthyes
#> 20 <U+00A6> <U+00A6>--Cephalaspidomorphi
#> 21 <U+00A6> <U+00B0>--Sarcopterygii
#> 22 <U+00B0>--Reptilia
Get a taxonomic tree of Fungi down to the phylum level
galah_call() |>
galah_identify("fungi") |>
galah_down_to(class) |>
atlas_taxonomy()
#> levelName
#> 1 Fungi
#> 2 <U+00A6>--Ascomycota
#> 3 <U+00A6> <U+00A6>--Ascomycetes
#> 4 <U+00A6> <U+00A6>--Discomycetes
#> 5 <U+00A6> <U+00A6>--Pezizomycotina
#> 6 <U+00A6> <U+00A6> <U+00A6>--Arthoniomycetes
#> 7 <U+00A6> <U+00A6> <U+00A6>--Dothideomycetes
#> 8 <U+00A6> <U+00A6> <U+00A6>--Eurotiomycetes
#> 9 <U+00A6> <U+00A6> <U+00A6>--Geoglossomycetes
#> 10 <U+00A6> <U+00A6> <U+00A6>--Laboulbeniomycetes
#> 11 <U+00A6> <U+00A6> <U+00A6>--Lecanoromycetes
#> 12 <U+00A6> <U+00A6> <U+00A6>--Leotiomycetes
#> 13 <U+00A6> <U+00A6> <U+00A6>--Lichinomycetes
#> 14 <U+00A6> <U+00A6> <U+00A6>--Orbiliomycetes
#> 15 <U+00A6> <U+00A6> <U+00A6>--Pezizomycetes
#> 16 <U+00A6> <U+00A6> <U+00A6>--Sordariomycetes
#> 17 <U+00A6> <U+00A6> <U+00B0>--Xylonomycetes
#> 18 <U+00A6> <U+00A6>--Saccharomycotina
#> 19 <U+00A6> <U+00A6> <U+00B0>--Saccharomycetes
#> 20 <U+00A6> <U+00A6>--Taphrinomycotina
#> 21 <U+00A6> <U+00A6> <U+00A6>--Neolectomycetes
#> 22 <U+00A6> <U+00A6> <U+00A6>--Pneumocystidomycetes
#> 23 <U+00A6> <U+00A6> <U+00A6>--Schizosaccharomycetes
#> 24 <U+00A6> <U+00A6> <U+00B0>--Taphrinomycetes
#> 25 <U+00A6> <U+00B0>--Pyrenomycete
#> 26 <U+00A6>--Basidiomycota
#> 27 <U+00A6> <U+00A6>--Agaricomycotina
#> 28 <U+00A6> <U+00A6> <U+00A6>--Agaricomycetes
#> 29 <U+00A6> <U+00A6> <U+00A6>--Dacrymycetes
#> 30 <U+00A6> <U+00A6> <U+00B0>--Tremellomycetes
#> 31 <U+00A6> <U+00A6>--Basidiomycetes
#> 32 <U+00A6> <U+00A6>--Entorrhizomycetes
#> 33 <U+00A6> <U+00A6>--Pucciniomycotina
#> 34 <U+00A6> <U+00A6> <U+00A6>--Agaricostilbomycetes
#> 35 <U+00A6> <U+00A6> <U+00A6>--Atractiellomycetes
#> 36 <U+00A6> <U+00A6> <U+00A6>--Classiculomycetes
#> 37 <U+00A6> <U+00A6> <U+00A6>--Cryptomycocolacomycetes
#> 38 <U+00A6> <U+00A6> <U+00A6>--Cystobasidiomycetes
#> 39 <U+00A6> <U+00A6> <U+00A6>--Microbotryomycetes
#> 40 <U+00A6> <U+00A6> <U+00A6>--Pucciniomycetes
#> 41 <U+00A6> <U+00A6> <U+00A6>--Spiculogloeomycetes
#> 42 <U+00A6> <U+00A6> <U+00A6>--Tritirachiomycetes
#> 43 <U+00A6> <U+00A6> <U+00B0>--Urediniomycetes
#> 44 <U+00A6> <U+00A6>--Ustilaginomycotina
#> 45 <U+00A6> <U+00A6> <U+00A6>--Exobasidiomycetes
#> 46 <U+00A6> <U+00A6> <U+00A6>--Malasseziomycetes
#> 47 <U+00A6> <U+00A6> <U+00A6>--Monilielliomycetes
#> 48 <U+00A6> <U+00A6> <U+00A6>--Ustilaginomycetes
#> 49 <U+00A6> <U+00A6> <U+00B0>--Ustomycetes
#> 50 <U+00A6> <U+00A6>--Wallemiomycetes
#> 51 <U+00A6> <U+00B0>--Wallemiomycotina
#> 52 <U+00A6> <U+00B0>--Wallemiomycetes
#> 53 <U+00A6>--Chytridiomycota
#> 54 <U+00A6> <U+00A6>--Blastocladiomycetes
#> 55 <U+00A6> <U+00A6>--Chytridiomycetes
#> 56 <U+00A6> <U+00A6>--Monoblepharidomycetes
#> 57 <U+00A6> <U+00B0>--Neocallimastigomycetes
#> 58 <U+00A6>--Glomeromycota
#> 59 <U+00A6> <U+00B0>--Glomeromycetes
#> 60 <U+00A6>--Microspora
#> 61 <U+00A6> <U+00B0>--Microsporea
#> 62 <U+00B0>--Zygomycota
#> 63 <U+00A6>--Entomophthoromycotina
#> 64 <U+00A6> <U+00A6>--Basidiobolomycetes
#> 65 <U+00A6> <U+00A6>--Entomophthoromycetes
#> 66 <U+00A6> <U+00B0>--Neozygitomycetes
#> 67 <U+00A6>--Trichomycetes
#> 68 <U+00B0>--Zygomycetes
The approach used by this function is recursive, meaning that it
becomes slow for large queries such as
atlas_taxonomy(search_taxa("Plantae"), down_to = galah_down_to(species)).
Although the inputs to search_taxa and down_to are
case-insensitive, node names are always returned in title case.
search_taxa() to search for an individual taxon;
show_all_ranks() for valid ranks used to specify the down_to
argument.