Used to
store classifications in reference to a taxonomic tree.
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
taxonomyoption. Can be any length, but must consist of valid indexes for taxa in thetaxonomyobject.
- taxonomy
A taxonomy object. Only needed if taxon indexes are supplied as the first argument.
- .names
The names of the vector.
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)
#> a b c d
#> "Panthera" "Panthera leo" "Panthera leo" "Panthera tigris"
#> e f g h
#> "Panthera tigris" "Ursidae" "Ursus arctos" "Ursus arctos"
#> i j k l
#> "Felidae" "Panthera tigris" "Ursidae" "Felidae"
tax_rank(x)
#> <taxon_rank[12]>
#> a b c d e f g h i j
#> genus species species species species family species species family species
#> k l
#> family family
#> Rank levels: order < family < genus < species
tax_id(x)
#> <taxon_id[12]>
#> a b c d e f
#> 9688 (ncbi) 9689 (ncbi) 9689 (ncbi) 9694 (ncbi) 9694 (ncbi) 9632 (ncbi)
#> g h i j k l
#> 9644 (ncbi) 9644 (ncbi) 9681 (ncbi) 9694 (ncbi) 9632 (ncbi) 9681 (ncbi)
tax_db(x)
#> <taxon_db[12]>
#> a b c d e f g h i j k l
#> ncbi ncbi ncbi ncbi ncbi ncbi ncbi ncbi ncbi ncbi ncbi ncbi
tax_auth(x)
#> <taxon_authority[12]>
#> a b c d e f
#> Oken 1816 L. 1758 L. 1758 L. 1758 L. 1758 Fischer 1817
#> g h i j k l
#> L. 1758 L. 1758 Fischer 1817 L. 1758 Fischer 1817 Fischer 1817
tax_author(x)
#> a b c d e f g h
#> "Oken" "L." "L." "L." "L." "Fischer" "L." "L."
#> i j k l
#> "Fischer" "L." "Fischer" "Fischer"
tax_date(x)
#> a b c d e f g h i j k
#> "1816" "1758" "1758" "1758" "1758" "1817" "1758" "1758" "1817" "1758" "1817"
#> l
#> "1817"
tax_cite(x)
#> a b c d e f g h i j k l
#> "" "" "" "" "" "" "" "" "" "" "" ""
# Manipulate classification vectors
x[1:3]
#> <classification[3]>
#> a b
#> Carnivora|Felidae|Panthera Carnivora|Felidae|Panthera|Panthera leo
#> c
#> Carnivora|Felidae|Panthera|Panthera leo
#> Rank levels: order < family < genus < species
x[tax_rank(x) > 'family']
#> <classification[8]>
#> a
#> Carnivora|Felidae|Panthera
#> b
#> Carnivora|Felidae|Panthera|Panthera leo
#> c
#> Carnivora|Felidae|Panthera|Panthera leo
#> d
#> Carnivora|Felidae|Panthera|Panthera tigris
#> e
#> Carnivora|Felidae|Panthera|Panthera tigris
#> g
#> Carnivora|Ursidae|Ursus|Ursus arctos
#> h
#> Carnivora|Ursidae|Ursus|Ursus arctos
#> j
#> Carnivora|Felidae|Panthera|Panthera tigris
#> Rank levels: order < family < genus < species
# c(x, x)
# x['b'] <- NA
is.na(x)
#> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
# as.data.frame(x)
# tibble::as_tibble(x)
# Use as columns in tables
tibble::tibble(x = x, y = 1:12)
#> # A tibble: 12 × 2
#> x y
#> <classif> <int>
#> 1 Carnivora|Felidae|Panthera 1
#> 2 Carnivora|Felidae|Panthera|Panthera leo 2
#> 3 Carnivora|Felidae|Panthera|Panthera leo 3
#> 4 Carnivora|Felidae|Panthera|Panthera tigris 4
#> 5 Carnivora|Felidae|Panthera|Panthera tigris 5
#> 6 Carnivora|Ursidae 6
#> 7 Carnivora|Ursidae|Ursus|Ursus arctos 7
#> 8 Carnivora|Ursidae|Ursus|Ursus arctos 8
#> 9 Carnivora|Felidae 9
#> 10 Carnivora|Felidae|Panthera|Panthera tigris 10
#> 11 Carnivora|Ursidae 11
#> 12 Carnivora|Felidae 12
data.frame(x = x, y = 1:12)
#> x y
#> 1 Carnivora|Felidae|Panthera 1
#> 2 Carnivora|Felidae|Panthera|Panthera leo 2
#> 3 Carnivora|Felidae|Panthera|Panthera leo 3
#> 4 Carnivora|Felidae|Panthera|Panthera tigris 4
#> 5 Carnivora|Felidae|Panthera|Panthera tigris 5
#> 6 Carnivora|Ursidae 6
#> 7 Carnivora|Ursidae|Ursus|Ursus arctos 7
#> 8 Carnivora|Ursidae|Ursus|Ursus arctos 8
#> 9 Carnivora|Felidae 9
#> 10 Carnivora|Felidae|Panthera|Panthera tigris 10
#> 11 Carnivora|Ursidae 11
#> 12 Carnivora|Felidae 12