Re-index elements of taxlist objects

The assignment of new identifiers must take into account all possible occurrences of such indices in taxlist objects in order to maintain their validity.

Usage

reindex(object, ...)

# S3 method for class 'taxlist'
reindex(object, old, new, idx = "TaxonConceptID", ...)

reindex(object, ...) <- value

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

Arguments

object

A taxlist object.

...

Further arguments to be passed among methods.

old

A vector with old identifiers to be re-indized. This may contain all identifiers or only a part of them. If only a part, the rest of indices will be preserved. If the changes insert duplicated identifiers, an error message will be retrieved. If missing, all identifiers in 'object' will be considered.

new, value

A vector with the new identifiers. It has to be of the same length as 'old'.

idx

Name of the index to be changed, which means "TaxonConceptID", "TaxonUsageID", or "ViewID" for taxon concepts, taxon usage names, or taxon views, respectively. You can also use the aliases "concept", "usage", and "view".

Value

An object of class taxlist with modified identifiers.

Examples

## Copy taxonomic list
sp_list <- Easplist
summary(sp_list, "papyrus")
#> ------------------------------ 
#> concept ID: 206 
#> view ID: 1 
#> level: species 
#> parent: 54853 Cyperus L. 
#> 
#> # accepted name: 
#> 206 Cyperus papyrus L. 
#> 
#> # synonyms (2): 
#> 52612 Cyperus papyrus ssp. antiquorum (Willd.) Chiov. 
#> 52613 Cyperus papyrus ssp. nyassicus Chiov. 
#> ------------------------------

## Re-index taxon concepts
reindex(sp_list) <- id_generator(nrow(sp_list@taxonRelations),
    mode = "character")

## Re-index taxon usage names
reindex(sp_list, idx = "TaxonUsageID") <- id_generator(nrow(sp_list@taxonNames),
    mode = "character")

## Re-index taxon views
reindex(sp_list, idx = "ViewID") <- id_generator(nrow(sp_list@taxonViews),
    mode = "character")

## Check result
validObject(sp_list)
#> [1] TRUE
summary(sp_list, "papyrus")
#> ------------------------------ 
#> concept ID: rHXCwew44L 
#> view ID: N9aUiE0CqO 
#> level: species 
#> parent: g5SrYoV6Aa Cyperus L. 
#> 
#> # accepted name: 
#> 4QVLsD2o82 Cyperus papyrus L. 
#> 
#> # synonyms (2): 
#> bd312F8F1d Cyperus papyrus ssp. antiquorum (Willd.) Chiov. 
#> 2AoWYUWb4O Cyperus papyrus ssp. nyassicus Chiov. 
#> ------------------------------