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Handle information on taxon usage names.

Source: R/taxon_names.R
taxon_names.Rd

The slot taxonNames in taxlist objects contains taxon usage names for the respective taxon. These functions assist on the access and modification of entries for names.

Usage

taxon_names(taxlist, ...)

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

taxon_names(taxlist, ...) <- value

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

add_synonym(taxlist, ...)

# S3 method for taxlist
add_synonym(taxlist, ConceptID, TaxonName, AuthorName, ...)

update_name(taxlist, ...)

# S3 method for taxlist
update_name(taxlist, UsageID, ...)

delete_name(taxlist, ...)

# S3 method for taxlist
delete_name(taxlist, UsageID, ...)

Arguments

taxlist

A taxlist object to be modified.

...

Further arguments passed among methods. In update_name are vectors including the variables to be updated for the respective taxon usage ID.

value

A data frame used as new slot taxonNames in taxlist.

ConceptID

Numeric vector indicating the concept ID to which the synonyms will be added.

TaxonName, AuthorName

Character values used for the new names (synonyms).

UsageID

Numeric vector indicating the taxon usage IDs to be updated.

Value

A data frame or, in the case of the replacement method, a taxlist object with modified slot taxonNames.

Details

The replacement method taxon_names<- is a quick alternative to include names in empty taxlist objects.

The function add_synonym() works only for adding names to existing taxon concepts. For adding new taxon concepts as well you should use add_concept().

See also

taxlist

Author

Miguel Alvarez kamapu78@gmail.com

Examples

## 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_names(Euclea)
#>      TaxonUsageID TaxonConceptID                       TaxonName
#> 297           269            269                Euclea divinorum
#> 298         50787            269 Euclea divinorum ssp. keniensis
#> 5043        55709          55707                          Euclea
#>              AuthorName
#> 297               Hiern
#> 298  (R. E. Fr.) de Wit
#> 5043                   

## Insert a synonym to Diospyros scabra
summary(Easplist, "Diospyros scabra")
#> ------------------------------ 
#> concept ID: 51793 
#> view ID: 1 
#> level: species 
#> parent: 55171 Diospyros L. 
#> 
#> # accepted name: 
#> 51793 Diospyros scabra (Chiov.) Cufod. 
#> ------------------------------
sp_list <- add_synonym(taxlist = Easplist, ConceptID = 51793,
  TaxonName = "Maba scabra", AuthorName = "Chiov.")
summary(sp_list, "Diospyros scabra")
#> ------------------------------ 
#> concept ID: 51793 
#> view ID: 1 
#> level: species 
#> parent: 55171 Diospyros L. 
#> 
#> # accepted name: 
#> 51793 Diospyros scabra (Chiov.) Cufod. 
#> 
#> # synonyms (1): 
#> 56139 Maba scabra Chiov. 
#> ------------------------------

## Delete a synonym of Launaea cornuta
summary(sp_list, "Launaea cornuta")
#> ------------------------------ 
#> concept ID: 355 
#> view ID: 1 
#> level: species 
#> parent: 54923 Launaea Cass. 
#> 
#> # accepted name: 
#> 355 Launaea cornuta (Hochst. ex Oliv. & Hiern) C. Jeffrey 
#> 
#> # synonyms (2): 
#> 53821 Sonchus exauriculatus (Oliv. & Hiern) O. Hoffm. 
#> 53843 Sonchus bipontini var. pinnatifidus Oliv. & Hiern 
#> ------------------------------
sp_list <- delete_name(sp_list, 53821)
summary(sp_list, "Launaea cornuta")
#> ------------------------------ 
#> concept ID: 355 
#> view ID: 1 
#> level: species 
#> parent: 54923 Launaea Cass. 
#> 
#> # accepted name: 
#> 355 Launaea cornuta (Hochst. ex Oliv. & Hiern) C. Jeffrey 
#> 
#> # synonyms (1): 
#> 53843 Sonchus bipontini var. pinnatifidus Oliv. & Hiern 
#> ------------------------------

## Hypothetical correction in author name in Launaea cornuta
sp_list <- update_name(taxlist = sp_list, UsageID = 355, AuthorName = "L.")
summary(sp_list, "Launaea cornuta")
#> ------------------------------ 
#> concept ID: 355 
#> view ID: 1 
#> level: species 
#> parent: 54923 Launaea Cass. 
#> 
#> # accepted name: 
#> 355 Launaea cornuta L. 
#> 
#> # synonyms (1): 
#> 53843 Sonchus bipontini var. pinnatifidus Oliv. & Hiern 
#> ------------------------------