taxlist (version 0.2.3)

accepted_name: Manage accepted names, synonyms and basionyms

Description

Taxon usage names for a taxon concept can be divided into three categories: accepted names, basionyms and synonyms. Each single taxon concept may at least have an accepted name, while basionym and synonyms are optional. The functions accepted_name, basionym and synonyms can be used either to display the respective usage names or to set usage names in one of those categories.

Usage

accepted_name(taxlist, ConceptID, ...)
# S4 method for taxlist,numeric
accepted_name(taxlist, ConceptID, show_traits = FALSE, ...)
# S4 method for taxlist,missing
accepted_name(taxlist, ConceptID, ...)
accepted_name(taxlist, ConceptID) <- value
# S4 method for taxlist,numeric,numeric
accepted_name(taxlist, ConceptID) <- value
synonyms(taxlist, ConceptID, ...)
# S4 method for taxlist,numeric
synonyms(taxlist, ConceptID, ...)
# S4 method for taxlist,missing
synonyms(taxlist, ConceptID, ...)
basionym(taxlist, ConceptID, ...)
# S4 method for taxlist,numeric
basionym(taxlist, ConceptID, ...)
# S4 method for taxlist,missing
basionym(taxlist, ConceptID, ...)
basionym(taxlist, ConceptID) <- value
# S4 method for taxlist,numeric,numeric
basionym(taxlist, ConceptID) <- value

Value

Most of the methods return information in data frames, while replacement methods do it as taxlist objects.

Arguments

taxlist

An object of class taxlist.

ConceptID

Integer containing concept IDs where to request or set names for one category.

...

Further arguments passed among methods.

show_traits

Logical value, whether traits should be included in the output of accepted_name or not.

value

Integer containing usage IDs to be set to the respective category in the respective taxon concept.

Author

Miguel Alvarez

Details

The function accepted_name retrieves the accepted names for the indicated taxon concepts or for the whole taxlist object. By using show_traits=TRUE, the respective taxon traits will be displayed as well, providing an overview of taxa included in the object. The replacement method for this function will set the respective usage name IDs as accepted names for the respective taxon concept, provided that these names are already set as synonyms in the respective concepts.

The function synonyms is working in a similar way as accepted_name, but this function does not include taxon traits in the output and there is no replacing method for synonyms. Alternatives for inserting new synonyms into a taxon concept are either moving synonyms from other taxa by using change_concept<- or inserting new names in the object by using add_synonym().

The function basionym is retrieving and setting basionyms in the respective taxon concepts similarly to accepted_name, but this function does not retrieve any information on taxon traits, either.

See Also

add_synonym() change_concept<-

Examples

## Set a different accepted name for Cyclosorus interruptus
summary(Easplist, "Cyclosorus interruptus")
accepted_name(Easplist, 50074) <- 53097
summary(Easplist, 50074)

## Inserting a new name first
summary(Easplist, "Basella alba")
Easplist <- add_synonym(
  taxlist = Easplist, ConceptID = 68,
  TaxonName = "Basella cordifolia", AuthorName = "Lam."
)
summary(Easplist, 68)
accepted_name(Easplist, 68) <- 56139
summary(Easplist, 68)