metacoder (version 0.3.7)

classifications: Get classifications of taxa

Description

Get character vector classifications of taxa in an object of type [taxonomy()] or [taxmap()] composed of data associated with taxa. Each classification is constructed by concatenating the data of the given taxon and all of its supertaxa.

obj$classifications(value = "taxon_names", sep = ";")
classifications(obj, value = "taxon_names", sep = ";")

Value

`character`

Arguments

obj

([taxonomy()] or [taxmap()])

value

What data to return. Any result of `all_names(obj)` can be used, but it usually only makes sense to data that corresponds to taxa 1:1, such as [taxon_ranks()]. By default, taxon indexes are returned.

sep

(`character` of length 1) The character(s) to place between taxon IDs

See Also

Other taxonomy data functions: id_classifications(), is_branch(), is_internode(), is_leaf(), is_root(), is_stem(), map_data(), map_data_(), n_leaves(), n_leaves_1(), n_subtaxa(), n_subtaxa_1(), n_supertaxa(), n_supertaxa_1(), taxon_ids(), taxon_indexes(), taxon_names(), taxon_ranks()

Examples

# Defualt settings returns taxon names separated by ;
classifications(ex_taxmap)

# Other values can be returned besides taxon names
classifications(ex_taxmap, value = "taxon_ids")

# The separator can also be changed
classifications(ex_taxmap, value = "taxon_ranks", sep = "||")