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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.

Usage

atlas_taxonomy(request = NULL, identify = NULL, down_to = NULL)

Arguments

request

optional data_rquest object: generated by a call to galah_call().

identify

data.frame: generated by a call to galah_identify().

down_to

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.

Value

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

Details

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.

Examples

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   ¦--Cephalochordata               
#> 3   ¦   °--Amphioxi                  
#> 4   ¦--Craniata                      
#> 5   ¦   °--Agnatha                   
#> 6   ¦       ¦--Cephalasipidomorphi   
#> 7   ¦       °--Myxini                
#> 8   ¦--Tunicata                      
#> 9   ¦   ¦--Appendicularia            
#> 10  ¦   ¦--Ascidiacea                
#> 11  ¦   °--Thaliacea                 
#> 12  °--Vertebrata                    
#> 13      °--Gnathostomata             
#> 14          ¦--Amphibia              
#> 15          ¦--Aves                  
#> 16          ¦--Mammalia              
#> 17          ¦--Pisces                
#> 18          ¦   ¦--Actinopterygii    
#> 19          ¦   ¦--Chondrichthyes    
#> 20          ¦   ¦--Cephalaspidomorphi
#> 21          ¦   °--Sarcopterygii     
#> 22          °--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   ¦--Ascomycota                     
#> 3   ¦   ¦--Ascomycetes                
#> 4   ¦   ¦--Discomycetes               
#> 5   ¦   ¦--Pezizomycotina             
#> 6   ¦   ¦   ¦--Arthoniomycetes        
#> 7   ¦   ¦   ¦--Dothideomycetes        
#> 8   ¦   ¦   ¦--Eurotiomycetes         
#> 9   ¦   ¦   ¦--Geoglossomycetes       
#> 10  ¦   ¦   ¦--Laboulbeniomycetes     
#> 11  ¦   ¦   ¦--Lecanoromycetes        
#> 12  ¦   ¦   ¦--Leotiomycetes          
#> 13  ¦   ¦   ¦--Lichinomycetes         
#> 14  ¦   ¦   ¦--Orbiliomycetes         
#> 15  ¦   ¦   ¦--Pezizomycetes          
#> 16  ¦   ¦   ¦--Sordariomycetes        
#> 17  ¦   ¦   °--Xylonomycetes          
#> 18  ¦   ¦--Saccharomycotina           
#> 19  ¦   ¦   °--Saccharomycetes        
#> 20  ¦   ¦--Taphrinomycotina           
#> 21  ¦   ¦   ¦--Neolectomycetes        
#> 22  ¦   ¦   ¦--Pneumocystidomycetes   
#> 23  ¦   ¦   ¦--Schizosaccharomycetes  
#> 24  ¦   ¦   °--Taphrinomycetes        
#> 25  ¦   °--Pyrenomycete               
#> 26  ¦--Basidiomycota                  
#> 27  ¦   ¦--Agaricomycotina            
#> 28  ¦   ¦   ¦--Agaricomycetes         
#> 29  ¦   ¦   ¦--Dacrymycetes           
#> 30  ¦   ¦   °--Tremellomycetes        
#> 31  ¦   ¦--Basidiomycetes             
#> 32  ¦   ¦--Entorrhizomycetes          
#> 33  ¦   ¦--Pucciniomycotina           
#> 34  ¦   ¦   ¦--Agaricostilbomycetes   
#> 35  ¦   ¦   ¦--Atractiellomycetes     
#> 36  ¦   ¦   ¦--Classiculomycetes      
#> 37  ¦   ¦   ¦--Cryptomycocolacomycetes
#> 38  ¦   ¦   ¦--Cystobasidiomycetes    
#> 39  ¦   ¦   ¦--Microbotryomycetes     
#> 40  ¦   ¦   ¦--Pucciniomycetes        
#> 41  ¦   ¦   ¦--Spiculogloeomycetes    
#> 42  ¦   ¦   ¦--Tritirachiomycetes     
#> 43  ¦   ¦   °--Urediniomycetes        
#> 44  ¦   ¦--Ustilaginomycotina         
#> 45  ¦   ¦   ¦--Exobasidiomycetes      
#> 46  ¦   ¦   ¦--Malasseziomycetes      
#> 47  ¦   ¦   ¦--Monilielliomycetes     
#> 48  ¦   ¦   ¦--Ustilaginomycetes      
#> 49  ¦   ¦   °--Ustomycetes            
#> 50  ¦   ¦--Wallemiomycetes            
#> 51  ¦   °--Wallemiomycotina           
#> 52  ¦       °--Wallemiomycetes        
#> 53  ¦--Chytridiomycota                
#> 54  ¦   ¦--Blastocladiomycetes        
#> 55  ¦   ¦--Chytridiomycetes           
#> 56  ¦   ¦--Monoblepharidomycetes      
#> 57  ¦   °--Neocallimastigomycetes     
#> 58  ¦--Glomeromycota                  
#> 59  ¦   °--Glomeromycetes             
#> 60  ¦--Microspora                     
#> 61  ¦   °--Microsporea                
#> 62  °--Zygomycota                     
#> 63      ¦--Entomophthoromycotina      
#> 64      ¦   ¦--Basidiobolomycetes     
#> 65      ¦   ¦--Entomophthoromycetes   
#> 66      ¦   °--Neozygitomycetes       
#> 67      ¦--Trichomycetes              
#> 68      °--Zygomycetes

See also

search_taxa() to search for an individual taxon; show_all_ranks() for valid ranks used to specify the down_to argument.