taxon_traits: Manipulation of taxon traits in taxlist objects.

In ropensci/taxlist: Handling Taxonomic Lists

Manipulation of taxon traits in taxlist objects.

Description

The slot taxonTraits in taxlist objects contains attributes of taxon concepts (e.g. functional traits). These functions are suitable for replacing, retrieving and appending trait information in taxonomic lists.

Usage

taxon_traits(taxlist, ...)

## S3 method for class 'taxlist'
taxon_traits(taxlist, ...)

taxon_traits(taxlist, ...) <- value

## S3 replacement method for class 'taxlist'
taxon_traits(taxlist, ...) <- value

update_trait(taxlist, ...)

## S3 method for class 'taxlist'
update_trait(taxlist, taxonTraits, ...)

Arguments

taxlist	A taxlist object.
...	Further arguments to be passed among methods.
value	Data frame to be set as slot taxonTraits.
taxonTraits	a data frame with taxon traits to be inserted in 'taxlist'. A column 'TaxonConceptID' is mandatory in this table. If some taxon concept IDs are not occurring in 'taxlist', an error message is retrieved by update_trait().

Details

Taxon traits are contained in a data frame at the slot taxonTraits in taxlist objects. To optimise space, this data frame contain only entries for those concepts with information, while taxa with no information are skipped from this table. Thus appending new variables may also have to include new rows in this slot, which is automatically carried out by this function.

The replacement method ⁠taxon_traits<-⁠ should be only used when constructing taxlist objects from an empty one.

Author(s)

Miguel Alvarez [e-mail]

See Also

taxlist.

Examples

## Displaying taxon traits
head(taxon_traits(Easplist))

## Updating traits for Launaea cornuta
summary(Easplist, "Launaea cornuta")
accepted_name(taxlist = Easplist, ConceptID = 355, show_traits = TRUE)

sp_list <- update_trait(taxlist = Easplist, taxonTraits = data.frame(
        TaxonConceptID = 355,
        life_form = "annual"))
accepted_name(taxlist = sp_list, ConceptID = 355, show_traits = TRUE)

ropensci/taxlist documentation built on Sept. 17, 2024, 3:39 p.m.