metacoder (version 0.3.7)

leaves: 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")

Value

`character`

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.

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)