An S4 class to represent taxonomic lists.

Class for taxonomic lists including synonyms, hierarchical ranks, parent-child relationships, taxon views and taxon traits.

Note that each taxon becomes an identifier, represented by the column TaxonConceptID in the slot taxonRelations, analogous to a primary key in a relational database. This identifier is restricted to an integer in taxlist and is specific for the object.

In the same way, each taxon usage name has an identifier in the column TaxonUsageID, slot taxonNames. The column ViewID in slot taxonViews is the identifier of the taxon view.

Slots

taxonNames

(data.frame) Table of taxon usage names (accepted names and synonyms).

taxonRelations

(data.frame) Relations between concepts, accepted names, basionyms, parents and hierarchical level.

taxonTraits

Table of taxon traits.

taxonViews

References used to determine the respective concept circumscription.

References

Alvarez M, Luebert F (2018). The taxlist package: managing plant taxonomic lists in R. Biodiversity Data Journal 6: e23635. doi:10.3897/bdj.6.e23635

Author

Miguel Alvarez

Examples

## Class 'taxlist'
showClass("taxlist")
#> Class "taxlist" [package "taxlist"]
#> 
#> Slots:
#>                                                                   
#> Name:      taxonNames taxonRelations     taxonViews    taxonTraits
#> Class:     data.frame     data.frame      df.lib_df     data.frame

## Create an empty object
sp_list <- new("taxlist")
sp_list
#> object size: 5.1 Kb 
#> validation of 'taxlist' object: TRUE 
#> 
#> number of taxon usage names: 0 
#> number of taxon concepts: 0 
#> trait entries: 0 
#> number of trait variables: 0 
#> taxon views: 0 
#>