Used to store information about taxa, such as names, ranks, and IDs.
Usage
taxon(name = character(0), rank = NA, id = NA, auth = NA, .names = NA, ...)Arguments
- name
The names of taxa. Inputs with be coerced into a character vector if anything else is given.
- rank
The ranks of taxa. Inputs with be coerced into a taxon_rank vector if anything else is given.
- id
The ids of taxa. These should be unique identifier and are usually associated with a database. Inputs with be coerced into a taxon_id vector if anything else is given.
- auth
The authority of the taxon. Inputs with be coerced into a taxon_authority vector if anything else is given.
- .names
The names of the vector.
- ...
Additional arguments.
See also
Other classes:
[.taxa_classification(),
classification(),
taxon_authority(),
taxon_db(),
taxon_id(),
taxon_rank()
Examples
# Create taxon name vector
x <- taxon(c('A', 'B', 'C'))
x <- taxon(name = c('Homo sapiens', 'Bacillus', 'Ascomycota', 'Ericaceae'),
rank = c('species', 'genus', 'phylum', 'family'),
id = taxon_id(c('9606', '1386', '4890', '4345'), db = 'ncbi'),
auth = c('Linnaeus, 1758', 'Cohn 1872', NA, 'Juss., 1789'))
names(x) <- c('a', 'b', 'c', 'd')
# Get parts of the taxon name vector
tax_name(x)
#> a b c d
#> "Homo sapiens" "Bacillus" "Ascomycota" "Ericaceae"
tax_rank(x)
#> <taxon_rank[4]>
#> a b c d
#> species genus phylum family
#> Rank levels: phylum < family < genus < species
tax_id(x)
#> <taxon_id[4]>
#> a b c d
#> 9606 (ncbi) 1386 (ncbi) 4890 (ncbi) 4345 (ncbi)
tax_db(x)
#> <taxon_db[4]>
#> a b c d
#> ncbi ncbi ncbi ncbi
tax_auth(x)
#> <taxon_authority[4]>
#> a b c d
#> Linnaeus 1758 Cohn 1872 NA Juss. 1789
tax_author(x)
#> a b c d
#> "Linnaeus" "Cohn" NA "Juss."
tax_date(x)
#> a b c d
#> "1758" "1872" "" "1789"
tax_cite(x)
#> a b c d
#> "" "" "" ""
# Set parts of the taxon name vector
tax_name(x) <- tolower(tax_name(x))
tax_rank(x)[1] <- NA
tax_name(x)['b'] <- 'Billy'
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')
tax_cite(x)[1] <- 'Linnaeus, C. (1771). Mantissa plantarum altera generum.'
# Manipulate taxon name vectors
x[1:3]
#> <taxon[3]>
#> a b
#> 9999|homo sapiens NA 1999 9999|Billy Joe 2013|genus
#> c
#> 9999|ascomycota Billy 1796|phylum
#> Rank levels: phylum < family < genus < species
x[tax_rank(x) > 'family']
#> <taxon[2]>
#> <NA> b
#> NA 9999|Billy Joe 2013|genus
#> Rank levels: phylum < family < genus < species
x['b'] <- NA
x[c('c', 'd')] <- 'unknown'
is.na(x)
#> [1] FALSE TRUE FALSE FALSE
# Use as columns in tables
tibble::tibble(x = x, y = 1:4)
#> # A tibble: 4 × 2
#> x y
#> <taxon> <int>
#> 1 9999|homo sapiens NA 1999 1
#> 2 NA 2
#> 3 unknown 3
#> 4 unknown 4
data.frame(x = x, y = 1:4)
#> x y
#> 1 9999|homo sapiens NA 1999 1
#> 2 NA 2
#> 3 unknown 3
#> 4 unknown 4
# Converting to tables
tibble::as_tibble(x)
#> # A tibble: 4 × 7
#> tax_name tax_rank tax_id tax_db tax_author tax_date tax_cite
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 homo sapiens NA 9999 itis NA 1999 Linnaeus, C. (1771). …
#> 2 NA NA NA NA NA NA NA
#> 3 unknown NA NA NA NA NA NA
#> 4 unknown NA NA NA NA NA NA
as_data_frame(x)
#> tax_name tax_rank tax_id tax_db tax_author tax_date
#> 1 homo sapiens <NA> 9999 itis <NA> 1999
#> 2 <NA> <NA> <NA> <NA> <NA> <NA>
#> 3 unknown <NA> <NA> <NA> <NA> <NA>
#> 4 unknown <NA> <NA> <NA> <NA> <NA>
#> tax_cite
#> 1 Linnaeus, C. (1771). Mantissa plantarum altera generum.
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>