metacoder (version 0.3.7)

leaves_apply: Apply function to leaves of each taxon

Description

Apply a function to the leaves of each taxon. This is similar to using [leaves()] with [lapply()] or [sapply()].

obj$leaves_apply(func, subset = NULL, recursive = TRUE,
  simplify = FALSE, value = "taxon_indexes", ...)
leaves_apply(obj, func, subset = NULL, recursive = TRUE,
  simplify = FALSE, value = "taxon_indexes", ...)

Arguments

obj

The [taxonomy()] or [taxmap()] object containing taxon information to be queried.

func

(`function`) The function to apply.

subset

Taxon IDs, TRUE/FALSE vector, or taxon indexes to use. 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 give to the function. Any result of `all_names(obj)` can be used, but it usually only makes sense to use data that has an associated taxon id.

...

Extra arguments are passed to the function `func`.

Examples

# Count number of leaves under each taxon or its subtaxa
leaves_apply(ex_taxmap, length)

# Count number of leaves under each taxon
leaves_apply(ex_taxmap, length, recursive = FALSE)

# Converting output of leaves to upper case
leaves_apply(ex_taxmap, value = "taxon_names", toupper)

# Passing arguments to the function
leaves_apply(ex_taxmap, value = "taxon_names", paste0, collapse = ", ")