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,
keep_synonyms = TRUE,
...
)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 value indicating whether parents of selected taxa should be included in the output or not. This argument passed to
get_parents().- keep_synonyms
A logical value indicating whether synonyms should be included or not.
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.
Author
Miguel Alvarez kamapu78@gmail.com
Examples
## Synonyms used in the Kenya_veg
Synonyms <- used_synonyms(Kenya_veg)
head(Synonyms)
#> SynonymID Synonym SynonymAuthor
#> 1 50168 Clerodendron johnstonii NA
#> 2 50222 Cyperus sesquiflorus ssp. appendiculatus (K. Schum.) Lye
#> 3 50277 Teclea nobilis Delile
#> 4 50297 Polystichum fuscopaleaceum Alston
#> 5 50304 Dombeya goetzenii K. Schum.
#> 6 50225 Solanum sessilistellatum Bitter
#> TaxonConceptID AcceptedNameID AcceptedName AcceptedNameAuthor
#> 1 50167 50167 Clerodendrum johnstonii Oliv.
#> 2 50221 50221 Cyperus afrosylvestris Lye
#> 3 50276 50276 Vepris nobilis (Delile) Mziray
#> 4 50296 50296 Polystichum discretum (D. Don) J. Sm.
#> 5 50303 50303 Dombeya torrida (J.F. Gmel.) Bamps
#> 6 50224 50224 Solanum nigriviolaceum Bitter
## Subset species list to used concepts
species <- used_concepts(Kenya_veg)
Kenya_veg@species
#> object size: 554 Kb
#> validation of 'taxlist' object: TRUE
#>
#> number of taxon usage names: 3164
#> number of taxon concepts: 2392
#> trait entries: 102
#> number of trait variables: 1
#> taxon views: 3
#>
#> concepts with parents: 2237
#> concepts with children: 957
#>
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family
#> number of concepts in level form: 0
#> number of concepts in level variety: 65
#> number of concepts in level subspecies: 52
#> number of concepts in level species: 1422
#> number of concepts in level complex: 0
#> number of concepts in level genus: 699
#> number of concepts in level family: 154
#>
species
#> object size: 395.8 Kb
#> validation of 'taxlist' object: TRUE
#>
#> number of taxon usage names: 2339
#> number of taxon concepts: 1573
#> trait entries: 97
#> number of trait variables: 1
#> taxon views: 3
#>
#> concepts with parents: 514
#> concepts with children: 138
#>
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family
#> number of concepts in level form: 0
#> number of concepts in level variety: 65
#> number of concepts in level subspecies: 52
#> number of concepts in level species: 1366
#> number of concepts in level complex: 0
#> number of concepts in level genus: 90
#> number of concepts in level family: 0
#>