Skip to contents

Management of concept views in taxonomic lists.

Source: R/taxon_views.R
taxon_views.Rd

Retrieve or replace slot taxonViews in an object of class taxlist

Usage

taxon_views(taxlist, ...)

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

taxon_views(taxlist, ...) <- value

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

add_view(taxlist, taxonViews, ...)

# S4 method for 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'.

Value

An object of class taxlist with added views.

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.

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. doi:10.1093/bioinformatics/15.2.149

See also

taxlist

Author

Miguel Alvarez kamapu78@gmail.com

Examples

## See existing views
taxon_views(Easplist)
#>   ViewID                                 secundum view_bibtexkey
#> 1      1            African Plant Database (2012)  CJBGSANBI2012
#> 2      2 Taxonomic Name Resolution Service (2018)       TNRS2018
#> 3      3                    The Plant List (2013)        TPL2013

## 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)
#>   ViewID                                 secundum view_bibtexkey
#> 1      1            African Plant Database (2012)  CJBGSANBI2012
#> 2      2 Taxonomic Name Resolution Service (2018)       TNRS2018
#> 3      3                    The Plant List (2013)        TPL2013
#> 4      4                    Beentje et al. (1952)           <NA>
#>                           Title
#> 1                          <NA>
#> 2                          <NA>
#> 3                          <NA>
#> 4 Flora of Tropical East Africa
#>                                                                   URL
#> 1                                                                <NA>
#> 2                                                                <NA>
#> 3                                                                <NA>
#> 4 http://www.kew.org/science/directory/projects/FloraTropEAfrica.html