taxon_views: Management of concept views in taxonomic lists.

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

Retrieve or replace slot taxonViews in an object of class taxlist.

Usage

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## S4 method for signature 'taxlist'
taxon_views(taxlist, ...)

taxon_views(taxlist) <- value

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

## S4 method for signature 'taxlist,numeric,numeric'
replace_view(taxlist, old_view, new_view,
	...)

Arguments

taxlist

A taxlist object.

value

An object of class 'data.frame' containing the references used to define the circumscription of taxon concepts included in 'taxlist'.

old_view,new_view

View IDs (numeric vector) to be replaced in slot 'taxonRelations' (new in exchange to old).

...

Further arguments to be passed among methods.

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 ([email protected]).

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. https://doi.org/10.1093/bioinformatics/15.2.149

See Also

taxlist.

Examples

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library(taxlist)
data(Easplist)

## See existing views
taxon_views(Easplist)

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

taxon_views(Easplist)

taxlist documentation built on July 2, 2018, 1:03 a.m.