supertaxa_apply: Apply function to supertaxa of each taxon

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

Apply function to supertaxa of each taxon

Description

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

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

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 of taxa 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 supertaxa one rank above the target taxa. If 'TRUE', return all the supertaxa of every supertaxa, etc. Positive numbers indicate the number of recursions (i.e. number of ranks above 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.
na	('logical') If 'TRUE', return 'NA' where information is not available.
...	Extra arguments are passed to the function.

Examples

# Get number of supertaxa that each taxon is contained in
supertaxa_apply(ex_taxmap, length)

# Get classifications for each taxon
# Note; this can be done with `classifications()` easier
supertaxa_apply(ex_taxmap, paste, collapse = ";", include_input = TRUE,
                value = "taxon_names")

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