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 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]]See also
Other classes:
classification(),
taxon(),
taxon_authority(),
taxon_db(),
taxon_id(),
taxon_rank()
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
#> <taxonomy[4]>
#> 1[b]: 9681|Felidae Fischer de Waldheim 1817|family
#> └─2[c]: 9688|Panthera Oken 1816|genus
#> ├─3[d]: 9689|Panthera leo L. 1758|species
#> └─4[e]: 9694|Panthera tigris L. 1758|species
#> Rank levels: order < family < genus < species
x['b'] # Names can also be used
#> <taxonomy[4]>
#> 1[b]: 9681|Felidae Fischer de Waldheim 1817|family
#> └─2[c]: 9688|Panthera Oken 1816|genus
#> ├─3[d]: 9689|Panthera leo L. 1758|species
#> └─4[e]: 9694|Panthera tigris L. 1758|species
#> Rank levels: order < family < genus < species
x[2:3, subtaxa = FALSE] # Disable subtaxa
#> <taxonomy[2]>
#> 1[b]: 9681|Felidae Fischer de Waldheim 1817|family
#> └─2[c]: 9688|Panthera Oken 1816|genus
#> Rank levels: order < family < genus < species
x[3, supertaxa = TRUE] # include supertaxa
#> <taxonomy[5]>
#> 1[a]: 33554|Carnivora Bowdich 1821|order
#> └─2[b]: 9681|Felidae Fischer de Waldheim 1817|family
#> └─3[c]: 9688|Panthera Oken 1816|genus
#> ├─4[d]: 9689|Panthera leo L. 1758|species
#> └─5[e]: 9694|Panthera tigris L. 1758|species
#> Rank levels: order < family < genus < species
x[is_leaf(x)] # Subset by logical vector
#> <taxonomy[3]>
#> 1[d]: 9689|Panthera leo L. 1758|species
#> 2[e]: 9694|Panthera tigris L. 1758|species
#> 3[h]: 9644|Ursus arctos L. 1758|species
#> Rank levels: order < family < genus < species
# Get parts of the taxonomy vector
tax_name(x)
#> a b c d
#> "Carnivora" "Felidae" "Panthera" "Panthera leo"
#> e f g h
#> "Panthera tigris" "Ursidae" "Ursus" "Ursus arctos"
tax_rank(x)
#> <taxon_rank[8]>
#> a b c d e f g h
#> order family genus species species family genus species
#> Rank levels: order < family < genus < species
tax_id(x)
#> <taxon_id[8]>
#> a b c d e f
#> 33554 (ncbi) 9681 (ncbi) 9688 (ncbi) 9689 (ncbi) 9694 (ncbi) 9632 (ncbi)
#> g h
#> 9639 (ncbi) 9644 (ncbi)
tax_db(x)
#> <taxon_db[8]>
#> a b c d e f g h
#> ncbi ncbi ncbi ncbi ncbi ncbi ncbi ncbi
tax_auth(x)
#> <taxon_authority[8]>
#> a b c
#> Bowdich 1821 Fischer de Waldheim 1817 Oken 1816
#> d e f
#> L. 1758 L. 1758 Fischer de Waldheim 1817
#> g h
#> L. 1758 L. 1758
tax_author(x)
#> a b c
#> "Bowdich" "Fischer de Waldheim" "Oken"
#> d e f
#> "L." "L." "Fischer de Waldheim"
#> g h
#> "L." "L."
tax_date(x)
#> a b c d e f g h
#> "1821" "1817" "1816" "1758" "1758" "1817" "1758" "1758"
tax_cite(x)
#> a b c d e f g h
#> "" "" "" "" "" "" "" ""
# 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)
#> # A tibble: 8 × 8
#> supertaxon tax_name tax_rank tax_id tax_db tax_author tax_date tax_cite
#> <int> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 NA carnivora NA 9999 itis NA 1999 NA
#> 2 1 felidae family 9999 itis Joe 2013 NA
#> 3 2 panthera genus 9999 itis Billy 1796 Linnaeu…
#> 4 3 panthera leo species 9999 itis NA 1899 NA
#> 5 3 panthera tigris species 9999 itis NA 1997 NA
#> 6 1 ursidae family 9999 itis NA 2003 NA
#> 7 6 ursus genus 9999 itis NA 1996 NA
#> 8 7 ursus arctos species 9999 itis NA 1859 NA
as_data_frame(x)
#> supertaxon tax_name tax_rank tax_id tax_db tax_author tax_date
#> 1 NA carnivora <NA> 9999 itis <NA> 1999
#> 2 1 felidae family 9999 itis Joe 2013
#> 3 2 panthera genus 9999 itis Billy 1796
#> 4 3 panthera leo species 9999 itis <NA> 1899
#> 5 3 panthera tigris species 9999 itis <NA> 1997
#> 6 1 ursidae family 9999 itis <NA> 2003
#> 7 6 ursus genus 9999 itis <NA> 1996
#> 8 7 ursus arctos species 9999 itis <NA> 1859
#> tax_cite
#> 1 <NA>
#> 2 <NA>
#> 3 Linnaeus, C. (1771). Mantissa plantarum altera generum.
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> 7 <NA>
#> 8 <NA>
# Get taxonomy attributes
subtaxa(x)
#> $a
#> b c d e f g h
#> 2 3 4 5 6 7 8
#>
#> $b
#> c d e
#> 3 4 5
#>
#> $c
#> d e
#> 4 5
#>
#> $d
#> named integer(0)
#>
#> $e
#> named integer(0)
#>
#> $f
#> g h
#> 7 8
#>
#> $g
#> h
#> 8
#>
#> $h
#> named integer(0)
#>
subtaxa(x, value = tax_name(x))
#> $a
#> b c d e
#> "felidae" "panthera" "panthera leo" "panthera tigris"
#> f g h
#> "ursidae" "ursus" "ursus arctos"
#>
#> $b
#> c d e
#> "panthera" "panthera leo" "panthera tigris"
#>
#> $c
#> d e
#> "panthera leo" "panthera tigris"
#>
#> $d
#> named character(0)
#>
#> $e
#> named character(0)
#>
#> $f
#> g h
#> "ursus" "ursus arctos"
#>
#> $g
#> h
#> "ursus arctos"
#>
#> $h
#> named character(0)
#>
subtaxa(x, value = as_taxon(x))
#> $a
#> <taxon[7]>
#> b c
#> 9999|felidae Joe 2013|family 9999|panthera Billy 1796|genus
#> d e
#> 9999|panthera leo NA 1899|species 9999|panthera tigris NA 1997|species
#> f g
#> 9999|ursidae NA 2003|family 9999|ursus NA 1996|genus
#> h
#> 9999|ursus arctos NA 1859|species
#> Rank levels: order < family < genus < species
#>
#> $b
#> <taxon[3]>
#> c d
#> 9999|panthera Billy 1796|genus 9999|panthera leo NA 1899|species
#> e
#> 9999|panthera tigris NA 1997|species
#> Rank levels: order < family < genus < species
#>
#> $c
#> <taxon[2]>
#> d e
#> 9999|panthera leo NA 1899|species 9999|panthera tigris NA 1997|species
#> Rank levels: order < family < genus < species
#>
#> $d
#> <taxon[0]>
#> Rank levels: order < family < genus < species
#>
#> $e
#> <taxon[0]>
#> Rank levels: order < family < genus < species
#>
#> $f
#> <taxon[2]>
#> g h
#> 9999|ursus NA 1996|genus 9999|ursus arctos NA 1859|species
#> Rank levels: order < family < genus < species
#>
#> $g
#> <taxon[1]>
#> h
#> 9999|ursus arctos NA 1859|species
#> Rank levels: order < family < genus < species
#>
#> $h
#> <taxon[0]>
#> Rank levels: order < family < genus < species
#>
n_subtaxa(x)
#> a b c d e f g h
#> 7 3 2 0 0 2 1 0
supertaxa(x)
#> $a
#> named integer(0)
#>
#> $b
#> a
#> 1
#>
#> $c
#> b a
#> 2 1
#>
#> $d
#> c b a
#> 3 2 1
#>
#> $e
#> c b a
#> 3 2 1
#>
#> $f
#> a
#> 1
#>
#> $g
#> f a
#> 6 1
#>
#> $h
#> g f a
#> 7 6 1
#>
n_supertaxa(x)
#> a b c d e f g h
#> 0 1 2 3 3 1 2 3
leaves(x)
#> $a
#> d e h
#> 4 5 8
#>
#> $b
#> d e
#> 4 5
#>
#> $c
#> d e
#> 4 5
#>
#> $d
#> named integer(0)
#>
#> $e
#> named integer(0)
#>
#> $f
#> h
#> 8
#>
#> $g
#> h
#> 8
#>
#> $h
#> named integer(0)
#>
n_leaves(x)
#> a b c d e f g h
#> 3 2 2 0 0 1 1 0
is_leaf(x)
#> a b c d e f g h
#> FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE
stems(x)
#> $a
#> named integer(0)
#>
is_stem(x)
#> a b c d e f g h
#> FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
roots(x)
#> a
#> 1
is_root(x)
#> a b c d e f g h
#> TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
internodes(x)
#> b f g
#> 2 6 7
is_internode(x)
#> a b c d e f g h
#> FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE