leaves: Get leaf taxa

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Get leaf taxa

Description

Return the leaf taxa for a [taxonomy()] or [taxmap()] object. Leaf taxa are taxa with no subtaxa.

obj$leaves(subset = NULL, recursive = TRUE, simplify = FALSE, value = "taxon_indexes")
leaves(obj, subset = NULL, recursive = TRUE, simplify = FALSE, value = "taxon_indexes")

Arguments

obj	The [taxonomy()] or [taxmap()] object containing taxon information to be queried.
subset	Taxon IDs, TRUE/FALSE vector, or taxon indexes to find leaves for. Default: All taxa in 'obj' will be used. Any variable name that appears in [all_names()] can be used as if it was a vector on its own.
recursive	('logical' or 'numeric') If 'FALSE', only return the leaves if they occur one rank below the target taxa. If 'TRUE', return all of the leaves for each taxon. Positive numbers indicate the number of recursions (i.e. number of ranks below the target taxon to return). '1' is equivalent to 'FALSE'. Negative numbers are equivalent to 'TRUE'.
simplify	('logical') If 'TRUE', then combine all the results into a single vector of unique values.
value	What data to return. This is usually the name of column in a table in 'obj$data'. Any result of 'all_names(obj)' can be used, but it usually only makes sense to data that corresponds to taxa 1:1, such as [taxon_ranks()]. By default, taxon indexes are returned.

Value

'character'

See Also

Other taxonomy indexing functions: branches(), internodes(), roots(), stems(), subtaxa(), supertaxa()

Examples

# Return indexes of leaf taxa
leaves(ex_taxmap)

# Return indexes for a subset of taxa
leaves(ex_taxmap, subset = 2:17)
leaves(ex_taxmap, subset = taxon_names == "Plantae")

# Return something besides taxon indexes
leaves(ex_taxmap, value = "taxon_names")
leaves(ex_taxmap, subset = taxon_ranks == "genus", value = "taxon_names")

# Return a vector of all unique values
leaves(ex_taxmap, value = "taxon_names", simplify = TRUE)

# Only return leaves for their direct supertaxa
leaves(ex_taxmap, value = "taxon_names", recursive = FALSE)

metacoder documentation built on April 4, 2023, 9:08 a.m.