Get subtaxa

Get subtaxa indexes for each taxon or another per-taxon value. Subtaxa are taxa contained within a taxon.

Usage

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

Arguments

x

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

subset

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

max_depth

The number of ranks to traverse. For example, max_depth = 1 returns only immediate subtaxa. By default (NULL) information for all subtaxa is returned (i.e. subtaxa of subtaxa, etc).

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.

...

Additional arguments.

See also

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

Other subtaxa functions: n_subtaxa()

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

# The indexes of immediate subtaxa (without subtaxa of subtaxa, etc) for each taxon
subtaxa(x, max_depth = 1)
#> [[1]]
#> [1] 2 6
#> 
#> [[2]]
#> [1] 3
#> 
#> [[3]]
#> [1] 4 5
#> 
#> [[4]]
#> integer(0)
#> 
#> [[5]]
#> integer(0)
#> 
#> [[6]]
#> [1] 7
#> 
#> [[7]]
#> [1] 8
#> 
#> [[8]]
#> integer(0)
#> 

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

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

# Only return data for some taxa (faster than subsetting the whole result)
subtaxa(x, subset = 3)
#> [[1]]
#> [1] 4 5
#>