[.taxa_classification | R Documentation |
Used to store information about a set of taxa forming a taxonomic tree.
## 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]]
taxa |
A taxon vector or something that can be converted to a taxon vector. |
supertaxa |
The indexes of |
.names |
The names of the vector (not the names of taxa). |
An S3
object of class taxa_taxon
Other classes:
classification()
,
taxon()
,
taxon_authority()
,
taxon_db()
,
taxon_id()
,
taxon_rank()
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)
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