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Search taxonomic trees

Source: R/atlas_taxonomy.R
atlas_taxonomy.Rd

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_request 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.

See also

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

Examples

# \donttest{
# 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              
# }