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Subset of taxlist objects will be done applying either logical operations or pattern matchings. Subsets can be referred to information contained either in the slot taxonNames, taxonRelations or taxonTraits.

Usage

# S4 method for class 'taxlist'
subset(
  x,
  subset,
  slot = "names",
  keep_children = FALSE,
  keep_parents = FALSE,
  ...
)

Arguments

x

Object of class taxlist.

subset

Logical vector or logical operation to apply as subset.

slot

Character value indicating the slot to be used for the subset.

keep_children

Logical value applied to hierarchical structures.

keep_parents

Logical value applied to hierarchical structures.

...

Further arguments to be passed to or from other methods.

Value

An object of class taxlist.

Details

The argument subset will be applied to the slot specified in argument slot. This argument also allows partial matchings.

Arguments keep_children and keep_parents are applied to objects including parent-child relationships. When those arguments are set as FALSE (the default), children or parents of selected taxon concepts will not be included in the subset.

Be aware that subset() won't work properly inside of function definitions.

Author

Miguel Alvarez kamapu78@gmail.com

Examples

## Produce a data set with only reed plants
sp_list <- subset(x = Easplist, subset = life_form == "reed_plant",
    slot = "taxonTraits", keep_parents = TRUE)
sp_list
#> object size: 22.3 Kb 
#> validation of 'taxlist' object: TRUE 
#> 
#> number of taxon usage names: 100 
#> number of taxon concepts: 27 
#> trait entries: 14 
#> number of trait variables: 1 
#> taxon views: 3 
#> 
#> concepts with parents: 24 
#> concepts with children: 13 
#> 
#> 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: 14
#> number of concepts in level complex: 0
#> number of concepts in level genus: 10
#> number of concepts in level family: 3
#> 

summary(as.factor(sp_list$life_form))
#> reed_plant       NA's 
#>         14         13