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 slottaxonRelations
.- 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()
.
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
#>
#> 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: 1
#> number of concepts in level complex: 0
#> number of concepts in level genus: 1
#> number of concepts in level family: 0
#>
taxon_relations(Euclea)
#> TaxonConceptID AcceptedName Basionym Parent Level ViewID
#> 267 269 269 NA 55707 species 1
#> 3537 55707 55709 NA NA genus NA