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

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

Arguments

taxlist

An object of class '>taxlist.

ConceptID

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

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.

...

Further arguments passed among methods.

Value

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

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.

Examples

Run this code

# NOT RUN {
library(taxlist)
data(Easplist)

## 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(Easplist, 68, TaxonName="Basella cordifolia",
	AuthorName="Lam.")
summary(Easplist, 68)
accepted_name(Easplist, 68) <- 56139
summary(Easplist, 68)

# }
# NOT RUN {
## attempt to use a name from another concept
accepted_name(Easplist, 50074) <- 51129
# }