Delete orphaned records

Manipulation of slots may generate orphaned entries in taxlist objects. The function clean deletes such entries and restores the consistency of the objects.

Usage

clean(object, ...)

# S4 method for class 'taxlist'
clean(object, times = 2, ...)

Arguments

object

A taxlist object.

...

Further arguments passed from or to other methods.

times

An integer indicating how many times the cleaning should be repeated.

Value

A clean taxlist object.

Details

Cleaning of objects will follow the deletion of orphaned names, orphaned taxon trait entries, and orphaned parent entries.

Author

Miguel Alvarez.

Examples

## Direct manipulation of slot taxonRelations generates an invalid object
Easplist@taxonRelations <- Easplist@taxonRelations[1:5, ]

## Now apply cleaning
Easplist <- clean(Easplist)
summary(Easplist)
#> object size: 7.8 Kb 
#> validation of 'taxlist' object: TRUE 
#> 
#> number of taxon usage names: 7 
#> number of taxon concepts: 5 
#> trait entries: 0 
#> number of trait variables: 1 
#> taxon views: 3 
#> 
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family 
#> number of concepts in level form: 0
#> number of concepts in level variety: 0
#> number of concepts in level subspecies: 0
#> number of concepts in level species: 5
#> number of concepts in level complex: 0
#> number of concepts in level genus: 0
#> number of concepts in level family: 0
#>