used_synonyms: Retrieve synonyms or taxon concepts used in a data set

Description

Plots records are rather linked to plant names than plant taxon concepts and used_synonyms() lists all synonyms linked to records in a vegtable object, including their respective accepted names.

On the other side, the function used_concepts() produces a subset of the taxonomic list embeded in the slot species including only taxonomic concepts linked to records in the slot samples.

Usage

used_synonyms(x, ...)
# S3 method for vegtable
used_synonyms(x, ...)
used_concepts(x, ...)
# S3 method for vegtable
used_concepts(x, keep_children = FALSE, keep_parents = FALSE, ...)

Value

The function used_synonyms() returns a data frame including following variables:

SynonymID: ID of the taxon usage name applied as synonym.
Synonym: The synonym itself.
SynonymAuthor: Author of synonym.
TaxonConceptID: ID of the respective taxon concept.
AcceptedNameID: ID of the taxon usage name set as accepted name of the taxon concept.
AcceptedName: The respective accepted name.
AcceptedNameAuthor: The author of the accepted name.

The function used_concepts() returns a taxlist object including only taxa occurring in the plot observations of the input vegtable

object.

Arguments

x: A vegtable object.
...: Further arguments to be passed from or to another methods.
keep_children: A logical argument indicating whether children of selected taxa should be included in the output or not. This argument passed to get_children().
keep_parents: A logical argument indicating whether parents of selected taxa should be included in the output or not. This argument passed to get_parents().

Author

Miguel Alvarez kamapu78@gmail.com

Examples

Run this code

## Synonyms used in the Kenya_veg
Synonyms <- used_synonyms(Kenya_veg)
head(Synonyms)

## Subset species list to used concepts
species <- used_concepts(Kenya_veg)
Kenya_veg@species
species