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Manipulation of taxon traits in taxlist objects.

Source: R/taxon_traits.R
taxon_traits.Rd

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 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.

See also

taxlist.

Author

Miguel Alvarez kamapu78@gmail.com

Examples

## Displaying taxon traits
head(taxon_traits(Easplist))
#>   TaxonConceptID          life_form
#> 1              7       phanerophyte
#> 2              9       phanerophyte
#> 3             18 facultative_annual
#> 4             20 facultative_annual
#> 5             21    obligate_annual
#> 6             22        chamaephyte

## Updating traits for Launaea cornuta
summary(Easplist, "Launaea cornuta")
#> ------------------------------ 
#> concept ID: 355 
#> view ID: 1 
#> level: species 
#> parent: 54923 Launaea Cass. 
#> 
#> # accepted name: 
#> 355 Launaea cornuta (Hochst. ex Oliv. & Hiern) C. Jeffrey 
#> 
#> # synonyms (2): 
#> 53821 Sonchus exauriculatus (Oliv. & Hiern) O. Hoffm. 
#> 53843 Sonchus bipontini var. pinnatifidus Oliv. & Hiern 
#> ------------------------------
accepted_name(taxlist = Easplist, ConceptID = 355, show_traits = TRUE)
#>   TaxonConceptID TaxonUsageID       TaxonName
#> 1            355          355 Launaea cornuta
#>                              AuthorName ViewID   Level     life_form
#> 1 (Hochst. ex Oliv. & Hiern) C. Jeffrey      1 species tussock_plant

sp_list <- update_trait(taxlist = Easplist, taxonTraits = data.frame(
        TaxonConceptID = 355,
        life_form = "annual"))
accepted_name(taxlist = sp_list, ConceptID = 355, show_traits = TRUE)
#>   TaxonConceptID TaxonUsageID       TaxonName
#> 1            355          355 Launaea cornuta
#>                              AuthorName ViewID   Level life_form
#> 1 (Hochst. ex Oliv. & Hiern) C. Jeffrey      1 species    annual