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 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