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Taxon rank class

Source: R/taxon_rank.R
taxon_rank.Rd

Maturing lifecycle Used to store taxon ranks, possibly associated with a taxonomy database. This is typically used to store taxon ranks in taxon objects.

Usage

taxon_rank(
  rank = character(),
  .names = NULL,
  levels = NULL,
  guess_order = TRUE
)

Arguments

rank

Zero or more taxonomic rank names. Inputs will be transformed to a character vector.

.names

The names of the vector

levels

A named numeric vector indicating the names and orders of possible taxonomic ranks. Higher numbers indicate for fine-scale groupings. Ranks of unknown order can be indicated with NA instead of a number.

guess_order

If TRUE and no rank order is given using numbers, try to guess order based on rank names.

Value

An S3 object of class taxa_taxon_rank

See also

Other classes: [.taxa_classification(), classification(), taxon(), taxon_authority(), taxon_db(), taxon_id()

Examples


# Making new objects
x <- taxon_rank(c('species', 'species', 'phylum', 'family'))

# Specifiying level order
taxon_rank(c('A', 'B', 'C', 'D', 'A', 'D', 'D'),
           levels = c('D', 'C', 'B', 'A'))
#> <taxon_rank[7]>
#> [1] A B C D A D D
#> Rank levels: D < C < B < A
taxon_rank(c('A', 'B', 'C', 'D', 'A', 'D', 'D'),
           levels = c(D = NA, A = 10, B = 20, C = 30))
#> <taxon_rank[7]>
#> [1] A B C D A D D
#> Rank levels: A < B < C ? D
names(x) <- c('a', 'b', 'c', 'd')

# Manipulating objects
as.character(x)
#>         a         b         c         d 
#> "species" "species"  "phylum"  "family" 
as.factor(x)
#>       a       b       c       d 
#> species species  phylum  family 
#> Levels: phylum family species
as.ordered(x)
#>       a       b       c       d 
#> species species  phylum  family 
#> Levels: phylum < family < species
x[2:3]
#> <taxon_rank[2]>
#>       b       c 
#> species  phylum 
#> Rank levels: phylum < family < species
x[x > 'family'] <- taxon_rank('unknown')
x[1] <- taxon_rank('order')
x['b']
#> <taxon_rank[1]>
#>       b 
#> unknown 
#> Rank levels: phylum < order < family < species ? unknown
x['b'] <- 'order'

# Using as columns in tables
tibble::tibble(x = x, y = 1:4)
#> # A tibble: 4 × 2
#>   x              y
#>   <tax_rank> <int>
#> 1 order          1
#> 2 order          2
#> 3 phylum         3
#> 4 family         4
data.frame(x = x, y = 1:4)
#>        x y
#> 1  order 1
#> 2  order 2
#> 3 phylum 3
#> 4 family 4

# Converting to tables
tibble::as_tibble(x)
#> # A tibble: 4 × 1
#>   tax_rank
#>   <chr>   
#> 1 order   
#> 2 order   
#> 3 phylum  
#> 4 family  
as_data_frame(x)
#>   tax_rank
#> 1    order
#> 2    order
#> 3   phylum
#> 4   family

# Trying to add an unknown level as a character causes an error
#x[2] <- 'superkingdom'

# But you can add a new level using taxon_rank objects
x[2] <- taxon_rank('superkingdom')