taxlist (version 0.2.4)

subset: Subset method for taxlist objects

Description

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,
  ...
)

Value

An object of class taxlist.

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.

Author

Miguel Alvarez

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.

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

summary(as.factor(sp_list$life_form))