Set and retrieves hierarchical levels

Taxonomic hierarchies can be set as levels in taxlist objects, ordered from lower to higher levels.

Add taxonomic levels for specific taxon concepts in a taxlist object. Also changes in concept circumscription may implicate changes in its taxonomic hierarchy.

Usage

levels(x)

# S3 method for class 'taxlist'
levels(x)

levels(x) <- value

# S3 method for class 'taxlist'
levels(x) <- value

Arguments

x

A taxlist object.

value

A character vector with replacement values for levels o x.

Value

A character vector or a taxlist object with added or modified taxonomic levels.

Details

Taxonomic levels will be handled as factors in the taxlist objects. Those levels are useful for creating subsets of related groups (e.g. by functions get_children() or get_parents()).

Levels in combination to parent-child relationships will be further used for checking consistency of taxonomic lists.

A replacement method of the form levels(x) <- value it is also implemented.

See also

prune_levels()

Author

Miguel Alvarez kamapu78@gmail.com

Examples

## Get levels of species list
levels(Easplist)
#> [1] "form"       "variety"    "subspecies" "species"    "complex"   
#> [6] "genus"      "family"    

## Add aggregate as new taxonomic level
levels(Easplist) <- c("form", "variety", "subspecies", "species", "complex",
    "aggregate", "genus", "family")
summary(Easplist)
#> object size: 761.5 Kb 
#> validation of 'taxlist' object: TRUE 
#> 
#> number of taxon usage names: 5393 
#> number of taxon concepts: 3887 
#> trait entries: 311 
#> number of trait variables: 1 
#> taxon views: 3 
#> 
#> concepts with parents: 3698 
#> concepts with children: 1343 
#> 
#> hierarchical levels: form < variety < subspecies < species < complex < aggregate < genus < family 
#> number of concepts in level form: 2
#> number of concepts in level variety: 95
#> number of concepts in level subspecies: 71
#> number of concepts in level species: 2521
#> number of concepts in level complex: 1
#> number of concepts in level aggregate: 0
#> number of concepts in level genus: 1011
#> number of concepts in level family: 186
#>