taxon_views: Management of concept views in taxonomic lists.

In ropensci/taxlist: Handling Taxonomic Lists

Management of concept views in taxonomic lists.

Description

Retrieve or replace slot taxonViews in an object of class taxlist

Usage

taxon_views(taxlist, ...)

## S3 method for class 'taxlist'
taxon_views(taxlist, ...)

taxon_views(taxlist, ...) <- value

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

add_view(taxlist, taxonViews, ...)

## S4 method for signature 'taxlist,data.frame'
add_view(taxlist, taxonViews, ...)

Arguments

taxlist	A taxlist object.
...	Further arguments to be passed among methods.
value	An object of class data.frame containing the references used to define the circumscription of taxon concepts included in taxlist.
taxonViews	A data frame with taxon views to be inserted in 'taxlist'.

Details

Taxon views indicate in taxlist objects the references determining the circumscription of the respective taxon concepts. When adding a new concept (see add_concept()), the respective reference may not yet occur in the input taxlist object.

The term taxon view was introduced by Zhong et al. (1996) and corresponds to the reference used for the definition of a concept.

This function retrieves the slot taxonViews from objects of the class taxlist.

The replacement method ⁠taxon_views<-⁠ replaces the whole content of slot taxonViews and it is only recommended to use when constructing a new taxlist object from an empty prototype.

Value

An object of class taxlist with added views.

Author(s)

Miguel Alvarez [e-mail]

References

Zhong Y, Jung S, Pramanik S, Beaman JH (1996). Data model and comparison and query methods for interacting classifications in a taxonomic database. Taxon 45: 223–241. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/15.2.149")}

See Also

taxlist

Examples

## See existing views
taxon_views(Easplist)

## Add a new view
sp_list <- add_view(taxlist = Easplist, taxonViews = data.frame(
        secundum = "Beentje et al. (1952)",
        Title = "Flora of Tropical East Africa",
        URL = "http://www.kew.org/science/directory/projects/FloraTropEAfrica.html"))

taxon_views(sp_list)

ropensci/taxlist documentation built on Sept. 17, 2024, 3:39 p.m.