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Retrieve or replace slot taxonRelations in taxlist objects

Source: R/taxon_relations.R, R/add_concept.R
taxon_relations.Rd

Retrieve the content of slot taxonRelations from a taxlist object or replace it by a new data frame.

Usage

taxon_relations(taxlist, ...)

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

taxon_relations(taxlist, ...) <- value

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

# S4 method for class 'taxlist,numeric'
update_concept(taxlist, ConceptID, ...)

Arguments

taxlist

A taxlist object.

...

Further arguments passed among methods.

value

A data.frame object to be set as slot taxonRelations.

ConceptID

Concept IDs to be updated.

Value

An object of class taxlist with added names and concepts.

Details

The replacement method taxon_relations<- should be only used when constructing taxlist objects from an empty one (prototype).

New concepts should be first added to a taxlist object using their respective accepted names. Synonyms can be further provided using the function add_synonym().

Additional named vectors can be provided to be included in slot taxonNames, in the cases where those variables already exist, otherwise they will be ignored.

It is recommended also to provide a concept view as ViewID (see taxon_views()). For adding a new view, use add_view().

See also

taxlist

Author

Miguel Alvarez kamapu78@gmail.com

Examples

## Subset for the genus Euclea and display of slot 'taxonNames'
Euclea <- subset(x = Easplist, subset = charmatch("Euclea", TaxonName),
  slot = "names", keep_children = TRUE)
Euclea
#> object size: 7 Kb 
#> validation of 'taxlist' object: TRUE 
#> 
#> number of taxon usage names: 3 
#> number of taxon concepts: 2 
#> trait entries: 0 
#> number of trait variables: 1 
#> taxon views: 3 
#> 
#> concepts with parents: 1 
#> concepts with children: 1 
#> 
#> concepts with rank information: 2 
#> concepts without rank information: 0 
#> 
#> family: 0
#>   genus: 1
#>     complex: 0
#>       species: 1
#>         subspecies: 0
#>           variety: 0
#>             form: 0
#> 
#> 
taxon_relations(Euclea)
#>      TaxonConceptID AcceptedName Basionym Parent   Level ViewID
#> 267             269          269       NA  55707 species      1
#> 3537          55707        55709       NA     NA   genus     NA