classification: Taxon class

In ropenscilabs/taxa: Classes for Storing and Manipulating Taxonomic Data

Taxon class

Description

\Sexpr[results=rd, stage=render]{taxa:::lifecycle("experimental")}

Used to store classifications in reference to a taxonomic tree.

Usage

classification(x = NULL, taxonomy = NULL, .names = NULL)

Arguments

x	One of: A list where each item represents a series of nested taxa. The contents of the list can be in any form that can be converted to a taxon vector. The indexes/names of each instance of a taxon in a taxonomy object specified by the taxonomy option. Can be any length, but must consist of valid indexes for taxa in the taxonomy object.
taxonomy	A taxonomy object. Only needed if taxon indexes are supplied as the first argument.
.names	The names of the vector.

Value

An S3 object of class taxa_classification

See Also

Other classes: [.taxa_classification(), taxon(), taxon_authority(), taxon_db(), taxon_id(), taxon_rank()

Examples

# Create classification vector with a list
x <- classification(list(
  c('Carnivora', 'Felidae', 'Panthera', 'Panthera leo'),
  c('Carnivora', 'Felidae', 'Panthera', 'Panthera tigris'),
  c('Carnivora', 'Ursidae', 'Ursus', 'Ursus arctos'),
  c('Carnivora', 'Ursidae', 'Ursus', 'Ursus arctos'),
  c('Carnivora', 'Felidae', 'Panthera', 'Panthera tigris')
))


# Create classification vector with indexes and a taxonomy
x <- classification(c(3, 4, 4, 5, 5, 6, 8, 8, 2, 5, 6, 2),
                    taxonomy(c('Carnivora', 'Felidae', 'Panthera', 'Panthera leo',
                               'Panthera tigris', 'Ursidae', 'Ursus', 'Ursus arctos'),
                             supertaxa = c(NA, 1, 2, 3, 3, 1, 6, 7)))

x <- classification(c(3, 4, 4, 5, 5, 6, 8, 8, 2, 5, 6, 2),
                    taxonomy(taxon(name = c('Carnivora', 'Felidae', 'Panthera', 'Panthera leo',
                                            'Panthera tigris', 'Ursidae', 'Ursus', 'Ursus arctos'),
                                   rank = c('order', 'family', 'genus', 'species',
                                            'species', 'family', 'genus', 'species'),
                                   id = taxon_id(c('33554', '9681', '9688', '9689',
                                                   '9694', '9632', '9639', '9644'),
                                                 db = 'ncbi'),
                                   auth = c('Bowdich, 1821', 'Fischer, 1817',
                                            'Oken, 1816', 'L., 1758',
                                            'L., 1758', 'Fischer, 1817',
                                            'L., 1758', 'L., 1758')),
                             supertaxa = c(NA, 1, 2, 3, 3, 1, 6, 7)))
names(x) <- letters[1:12]


# Get parts of the classification vector
tax_name(x)
tax_rank(x)
tax_id(x)
tax_db(x)
tax_auth(x)
tax_author(x)
tax_date(x)
tax_cite(x)

# Manipulate classification vectors
x[1:3]
x[tax_rank(x) > 'family']
# c(x, x)
# x['b'] <- NA
is.na(x)
# as.data.frame(x)
# tibble::as_tibble(x)

# Use as columns in tables
tibble::tibble(x = x, y = 1:12)
data.frame(x = x, y = 1:12)

ropenscilabs/taxa documentation built on Feb. 23, 2024, 6:31 p.m.