taxonomy: Taxonomy class

In taxa: Classes for Storing and Manipulating Taxonomic Data

Taxonomy class

Description

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

Used to store information about a set of taxa forming a taxonomic tree.

Usage

## S3 method for class 'taxa_classification'
x[...]

## S3 method for class 'taxa_classification'
x[[i]]

taxonomy(taxa = taxon(), supertaxa = NA, .names = NULL)

## S3 method for class 'taxa_taxonomy'
names(x)

## S3 replacement method for class 'taxa_taxonomy'
names(x) <- value

## S3 method for class 'taxa_taxonomy'
x[..., subtaxa = TRUE, supertaxa = FALSE, invert = FALSE]

## S3 method for class 'taxa_taxonomy'
x[[i, ..., subtaxa = TRUE, supertaxa = FALSE, invert = FALSE]]

Arguments

taxa	A taxon vector or something that can be converted to a taxon vector.
supertaxa	The indexes of taxa for each taxon's supertaxon.
.names	The names of the vector (not the names of taxa).

Value

An S3 object of class taxa_taxon

See Also

Other classes: classification(), taxon_authority(), taxon_db(), taxon_id(), taxon_rank(), taxon()

Examples

x <- taxonomy(c('Carnivora', 'Felidae', 'Panthera', 'Panthera leo',
                'Panthera tigris', 'Ursidae', 'Ursus', 'Ursus arctos'),
              supertaxa = c(NA, 1, 2, 3, 3, 1, 6, 7))

x <- 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 de Waldheim, 1817', 'Oken, 1816', 'L., 1758',
                             'L., 1758', 'Fischer de Waldheim, 1817', 'L., 1758', 'L., 1758')),
              supertaxa = c(NA, 1, 2, 3, 3, 1, 6, 7))
names(x) <- letters[1:8]

# Subset taxonomy vector
x[2] # By default, all subtaxa are included
x['b'] # Names can also be used
x[2:3, subtaxa = FALSE] # Disable subtaxa
x[3, supertaxa = TRUE] # include supertaxa
x[is_leaf(x)] # Subset by logical vector

# Get parts of the taxonomy 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)

# Set parts of the taxonomy vector
tax_name(x) <- tolower(tax_name(x))
tax_rank(x)[1] <- NA
tax_id(x) <- '9999'
tax_db(x) <- 'itis'
tax_auth(x) <- NA
tax_author(x)[2:3] <- c('Joe', 'Billy')
tax_date(x) <- c('1999', '2013', '1796', '1899',
                 '1997', '2003', '1996', '1859')
tax_cite(x)['c'] <- 'Linnaeus, C. (1771). Mantissa plantarum altera generum.'

# Convert to table
tibble::as_tibble(x)
as_data_frame(x)

# Get taxonomy attributes
subtaxa(x)
subtaxa(x, value = tax_name(x))
subtaxa(x, value = as_taxon(x))
n_subtaxa(x)
supertaxa(x)
n_supertaxa(x)
leaves(x)
n_leaves(x)
is_leaf(x)
stems(x)
is_stem(x)
roots(x)
is_root(x)
internodes(x)
is_internode(x)

taxa documentation built on April 12, 2022, 9:06 a.m.