View source: R/classification.R
classification | R Documentation |
Used to store classifications in reference to a taxonomic tree.
classification(x = NULL, taxonomy = NULL, .names = NULL)
x |
One of:
|
taxonomy |
A taxonomy object. Only needed if taxon indexes are supplied as the first argument. |
.names |
The names of the vector. |
An S3
object of class taxa_classification
Other classes:
[.taxa_classification()
,
taxon_authority()
,
taxon_db()
,
taxon_id()
,
taxon_rank()
,
taxon()
# 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)
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