accepted_name: Manage accepted names, synonyms and basionyms

In kamapu/taxlist: Handling Taxonomic Lists

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 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. 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.

The fucntion ⁠change_concept<-⁠ replace a taxon usage name (argument 'UsageID') to a different taxonomic concept (argument 'value').

Usage

accepted_name(taxlist, ...)

## S3 method for class 'taxlist'
accepted_name(taxlist, ConceptID, show_traits = FALSE, ...)

accepted_name(taxlist, ...) <- value

## S3 replacement method for class 'taxlist'
accepted_name(taxlist, ConceptID, ...) <- value

synonyms(taxlist, ...)

## S3 method for class 'taxlist'
synonyms(taxlist, ConceptID, ...)

basionym(taxlist, ...)

## S3 method for class 'taxlist'
basionym(taxlist, ConceptID, ...)

basionym(taxlist, ...) <- value

## S3 replacement method for class 'taxlist'
basionym(taxlist, ConceptID, ...) <- value

change_concept(taxlist, ...) <- value

## S3 replacement method for class 'taxlist'
change_concept(taxlist, UsageID, ...) <- value

Arguments

taxlist	An object of class taxlist.
...	Further arguments passed among methods.
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.
UsageID	Numeric vector with taxon usage IDs that will be changed to a different taxonomic concept.

Value

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

Author(s)

Miguel Alvarez [e-mail]

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)

## Display synonyms
head(synonyms(taxlist = Easplist))

## Synonyms for an specific concept
synonyms(taxlist = Easplist, ConceptID = 20)

## Basionym for Cyclosrus interruptus
summary(Easplist, 50074)
basionym(Easplist, 50074) <- 53097

summary(Easplist, 50074)
basionym(Easplist, 50074)

## Move the name Typha aethiopica to concept 573 (T. latifolia)
summary(Easplist, c(50105, 573))
change_concept(Easplist, 53130) <- 573
summary(Easplist, c(50105, 573))

kamapu/taxlist documentation built on Feb. 17, 2024, 8:27 a.m.