metacoder (version 0.3.7)

subtaxa_apply: Apply function to subtaxa of each taxon

Description

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

obj$subtaxa_apply(func, subset = NULL, recursive = TRUE,
  simplify = FALSE, include_input = FALSE, value = "taxon_indexes", ...)
subtaxa_apply(obj, func, subset = NULL, recursive = TRUE,
  simplify = FALSE, include_input = 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 subtaxa one rank below the target taxa. If `TRUE`, return all the subtaxa of every subtaxa, etc. 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.

include_input

(`logical`) If `TRUE`, the input taxa are included in the output

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.

Examples

# Count number of subtaxa in each taxon
subtaxa_apply(ex_taxmap, length)

# Paste all the subtaxon names for each taxon
subtaxa_apply(ex_taxmap, value = "taxon_names",
              recursive = FALSE, paste0, collapse = ", ")