For statistical purposes it may be necessary to insert information on recorded taxa into the slot samples, which contain the records of taxa in sampling plots. This can be also done selectivelly for specific taxonomic ranks and lower ranks can be aggregated to their parental ones.
If column TaxonConceptID is already existing in 'objec@samples',
this column will get overwritten, retrieving a warning message.
Usage
taxa2samples(object, ...)
# S3 method for vegtable
taxa2samples(
object,
merge_to,
include_levels,
add_relations = FALSE,
add_traits = FALSE,
...
)Arguments
- object
A vegtable object.
- ...
Further arguments passed among methods.
- merge_to
Character value indicating the level (taxonomic rank) to which taxa of lower rank have to be merged.
- include_levels
Character vector indicating the levels to be considered in the output object. This will set the values of TaxonConceptID and any respective values inserted from slots taxonRelations and taxonTraits as NA.
- add_relations
A logical value indicating whether the content of slot taxonRelations have to be inserted in slot samples or not.
- add_traits
A logical value indicating whether the content of slot taxonTraits have to be inserted in slot samples or not.
Value
An object of class vegtable.
Author
Miguel Alvarez kamapu78@gmail.com
Examples
## Add only variable TaxonConceptID
veg <- taxa2samples(Kenya_veg)
head(veg@samples)
#> TaxonUsageID ReleveID COVER_CODE LAYER SOCIABILIT INDIVID br_bl b_bbds
#> 1 18 358 + 0 <NA> <NA> + <NA>
#> 2 18 470 + 0 <NA> <NA> + <NA>
#> 3 18 1634 + 0 <NA> <NA> + <NA>
#> 4 18 587 + 0 <NA> <NA> + <NA>
#> 5 18 1949 2m 0 <NA> <NA> <NA> 2m
#> 6 18 1777 + 0 <NA> <NA> + <NA>
#> TaxonConceptID
#> 1 18
#> 2 18
#> 3 18
#> 4 18
#> 5 18
#> 6 18
## Add also information from slots taxonRelations and taxonTraits
veg <- taxa2samples(Kenya_veg, add_relations = TRUE, add_traits = TRUE)
head(veg@samples)
#> TaxonUsageID ReleveID COVER_CODE LAYER SOCIABILIT INDIVID br_bl b_bbds
#> 1 18 358 + 0 <NA> <NA> + <NA>
#> 2 18 470 + 0 <NA> <NA> + <NA>
#> 3 18 1634 + 0 <NA> <NA> + <NA>
#> 4 18 587 + 0 <NA> <NA> + <NA>
#> 5 18 1949 2m 0 <NA> <NA> <NA> 2m
#> 6 18 1777 + 0 <NA> <NA> + <NA>
#> TaxonConceptID Parent Level ViewID uri Basionym AcceptedName
#> 1 18 54759 species 1 <NA> NA 18
#> 2 18 54759 species 1 <NA> NA 18
#> 3 18 54759 species 1 <NA> NA 18
#> 4 18 54759 species 1 <NA> NA 18
#> 5 18 54759 species 1 <NA> NA 18
#> 6 18 54759 species 1 <NA> NA 18
#> lf_behn_2018
#> 1 facultative_annual
#> 2 facultative_annual
#> 3 facultative_annual
#> 4 facultative_annual
#> 5 facultative_annual
#> 6 facultative_annual
## Different ranks recorded at samples
veg <- taxa2samples(Kenya_veg, add_relations = TRUE)
summary(veg@samples$Level)
#> form variety subspecies species complex genus family
#> 0 2489 2453 68685 0 914 0
## Aggregate taxa to family level
veg <- taxa2samples(Kenya_veg, add_relations = TRUE, merge_to = "family")
summary(veg@samples$Level)
#> form variety subspecies species complex genus family
#> 0 0 0 0 0 0 74531
#> NA's
#> 10