subtaxa: Get subtaxa

In taxa: Classes for Storing and Manipulating Taxonomic Data

Get subtaxa

Description

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)

# The indexes of immediate subtaxa (without subtaxa of subtaxa, etc) for each taxon
subtaxa(x, max_depth = 1)

# Return something other than index
subtaxa(x, value = tax_name(x))

# Include each taxon with its subtaxa
subtaxa(x, value = tax_name(x), include = TRUE)

# Only return data for some taxa (faster than subsetting the whole result)
subtaxa(x, subset = 3)

taxa documentation built on April 12, 2022, 9:06 a.m.