Get supertaxa

Get supertaxa indexes for each taxon or another per-taxon value. Supertaxa are taxa a taxon is contained in.

Usage

supertaxa(
  x,
  subset = NULL,
  max_depth = NULL,
  include = FALSE,
  value = NULL,
  use_na = FALSE,
  ...
)

Arguments

x

The object to get supertaxa for, such as a taxonomy object.

subset

The subset of the tree to search for roots to that subset. Can be indexes or names.

max_depth

The number of levels to traverse. For example, max_depth = 1 returns only immediate supertaxa. By default (NULL) information for all supertaxa is returned.

include

If TRUE, include information for each taxon in the output.

value

Something to return instead of indexes. Must be the same length as the number of taxa.

use_na

Add a NA to represent the root of the taxonomy (i.e. no supertaxon)

...

Additional arguments.

See also

Other taxonomy functions: internodes(), leaves(), roots(), stems(), subtaxa()

Other supertaxa functions: n_supertaxa()

Examples

# Generate example data
x <- taxonomy(c('Carnivora', 'Felidae', 'Panthera', 'Panthera leo',
                'Panthera tigris', 'Ursidae', 'Ursus', 'Ursus arctos'),
              supertaxa = c(NA, 1, 2, 3, 3, 1, 6, 7))

# The indexes of all supertaxa (with supertaxa of supertaxa, etc) for each taxon
supertaxa(x)
#> [[1]]
#> integer(0)
#> 
#> [[2]]
#> [1] 1
#> 
#> [[3]]
#> [1] 2 1
#> 
#> [[4]]
#> [1] 3 2 1
#> 
#> [[5]]
#> [1] 3 2 1
#> 
#> [[6]]
#> [1] 1
#> 
#> [[7]]
#> [1] 6 1
#> 
#> [[8]]
#> [1] 7 6 1
#> 

# Return something other than index
supertaxa(x, value = tax_name(x))
#> [[1]]
#> character(0)
#> 
#> [[2]]
#> [1] "Carnivora"
#> 
#> [[3]]
#> [1] "Felidae"   "Carnivora"
#> 
#> [[4]]
#> [1] "Panthera"  "Felidae"   "Carnivora"
#> 
#> [[5]]
#> [1] "Panthera"  "Felidae"   "Carnivora"
#> 
#> [[6]]
#> [1] "Carnivora"
#> 
#> [[7]]
#> [1] "Ursidae"   "Carnivora"
#> 
#> [[8]]
#> [1] "Ursus"     "Ursidae"   "Carnivora"
#> 

# Include each taxon with its supertaxa
supertaxa(x, value = tax_name(x), include = TRUE)
#> [[1]]
#> [1] "Carnivora"
#> 
#> [[2]]
#> [1] "Felidae"   "Carnivora"
#> 
#> [[3]]
#> [1] "Panthera"  "Felidae"   "Carnivora"
#> 
#> [[4]]
#> [1] "Panthera leo" "Panthera"     "Felidae"      "Carnivora"   
#> 
#> [[5]]
#> [1] "Panthera tigris" "Panthera"        "Felidae"         "Carnivora"      
#> 
#> [[6]]
#> [1] "Ursidae"   "Carnivora"
#> 
#> [[7]]
#> [1] "Ursus"     "Ursidae"   "Carnivora"
#> 
#> [[8]]
#> [1] "Ursus arctos" "Ursus"        "Ursidae"      "Carnivora"   
#> 

# Only return data for some taxa (faster than subsetting the whole result)
supertaxa(x, subset = 3)
#> [[1]]
#> [1] 2 1
#>