Taxonomic classification can be included in taxlist
objects within the information provided at slot taxonRelations.
Nevertheless, for statistical analyses it may be more convenient to insert
such information in the slot taxonTraits.
Usage
tax2traits(object, ...)
# S3 method for class 'taxlist'
tax2traits(object, get_names = FALSE, ...)Arguments
- object
An object of class taxlist.
- ...
Further arguments to be passed among methods.
- get_names
Logical value indicating whether taxon names should be retrieved instead of taxon IDs.
Value
An object of class taxlist with taxonomy added as traits.
Details
This function can only be applied to objects containing parent-child relationships and information on taxonomic levels.
Author
Miguel Alvarez kamapu78@gmail.com.
Examples
## Family Acanthaceae with children
Acanthaceae <- subset(x = Easplist, subset = TaxonName == "Acanthaceae",
slot = "names", keep_children = TRUE)
summary(Acanthaceae)
#> object size: 29.9 Kb
#> validation of 'taxlist' object: TRUE
#>
#> number of taxon usage names: 143
#> number of taxon concepts: 113
#> trait entries: 9
#> number of trait variables: 1
#> taxon views: 3
#>
#> concepts with parents: 112
#> concepts with children: 28
#>
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family
#> number of concepts in level form: 0
#> number of concepts in level variety: 2
#> number of concepts in level subspecies: 3
#> number of concepts in level species: 84
#> number of concepts in level complex: 0
#> number of concepts in level genus: 23
#> number of concepts in level family: 1
#>
## Insert taxonomy to taxon traits
Acanthaceae <- tax2traits(Acanthaceae, get_names = TRUE)
head(taxon_traits(Acanthaceae))
#> TaxonConceptID life_form variety subspecies species
#> 14 59 obligate_annual <NA> <NA> Asystasia gangetica
#> 15 60 obligate_annual <NA> <NA> Asystasia mysurensis
#> 97 319 obligate_annual <NA> <NA> Hygrophila auriculata
#> 108 341 phanerophyte <NA> <NA> Justicia betonica
#> 238 50264 climbing_plant <NA> <NA> Thunbergia alata
#> 241 50423 phanerophyte <NA> <NA> Hypoestes aristata
#> genus family
#> 14 Asystasia Acanthaceae
#> 15 Asystasia Acanthaceae
#> 97 Hygrophila Acanthaceae
#> 108 Justicia Acanthaceae
#> 238 Thunbergia Acanthaceae
#> 241 Hypoestes Acanthaceae