supertaxa: Get all supertaxa of a taxon

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

Get all supertaxa of a taxon

Description

Return data for supertaxa (i.e. all taxa the target taxa are a part of) of each taxon in a [taxonomy()] or [taxmap()] object.

obj$supertaxa(subset = NULL, recursive = TRUE,
  simplify = FALSE, include_input = FALSE,
  value = "taxon_indexes", na = FALSE)
supertaxa(obj, 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.
subset	Taxon IDs, TRUE/FALSE vector, or taxon indexes to find supertaxa 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 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 return. Any result of [all_names()] 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.

Value

If 'simplify = FALSE', then a list of vectors are returned corresponding to the 'subset' argument. If 'simplify = TRUE', then unique values are returned in a single vector.

See Also

Other taxonomy indexing functions: branches(), internodes(), leaves(), roots(), stems(), subtaxa()

Examples

# return the indexes for supertaxa for each taxon
supertaxa(ex_taxmap)

# Only return data for some taxa using taxon indexes
supertaxa(ex_taxmap, subset = 1:3)

# Only return data for some taxa using taxon ids
supertaxa(ex_taxmap, subset = c("d", "e"))

# Only return data for some taxa using logical tests
supertaxa(ex_taxmap, subset = taxon_ranks == "species")

# Only return supertaxa one level above
supertaxa(ex_taxmap, recursive = FALSE)

# Only return supertaxa some number of ranks above
supertaxa(ex_taxmap, recursive = 2)

# Return something besides taxon indexes
supertaxa(ex_taxmap, value = "taxon_names")

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