subtaxa_apply: Apply function to subtaxa of each taxon

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

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 = ", ")

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