Produce subsets of vegtable objects.
Logical operations can be applied either to the plots, or the relations, which are the main slots in that class.
This method can be referred to the slot species the same way as
taxlist::subset(), then the rest of the data will include only
references to the subset of species list.
Usage
# S4 method for vegtable
subset(
x,
subset,
slot = "header",
keep_children = FALSE,
keep_parents = FALSE,
relation,
...
)Arguments
- x
A vegtable object for subset.
- subset
Logical expression for the subset.
- slot
Character value indicating the slot used as reference for subset. At the moment only the values "taxonNames", "taxonRelations", "taxonTraits", "header", "samples", and "relations" are accepted. The three first values will be applied to the respective slots in the contained taxlist object (slot species).
- keep_children
Argument passed to
taxlist::get_children().- keep_parents
Argument passed to
taxlist::get_parents().- relation
Character value indicating the relation (slot relations) to be used as reference for subset.
- ...
Further arguments passed from or to other methods.
Value
A S4 object of class vegtable.
Author
Miguel Alvarez kamapu78@gmail.com
Examples
## Subset by taxon name
Kenya_sub <- subset(
x = Kenya_veg, subset = TaxonName == "Tagetes",
slot = "taxonNames", keep_children = TRUE, keep_parents = TRUE
)
summary(Kenya_sub)
#> ## Metadata
#> db_name: Sweadataveg
#> sp_list: Easplist
#> dictionary: Swea
#> object size: 803 Kb
#> validity: TRUE
#>
#> ## Content
#> number of plots: 1946
#> plots with records: 48
#> variables in header: 34
#> number of relations: 3
#>
#> ## Taxonomic List
#> taxon names: 3
#> taxon concepts: 3
#> validity: TRUE
#>
summary(Kenya_sub@species)
#> object size: 7.5 Kb
#> validation of 'taxlist' object: TRUE
#>
#> number of taxon usage names: 3
#> number of taxon concepts: 3
#> trait entries: 1
#> number of trait variables: 1
#> taxon views: 3
#>
#> concepts with parents: 2
#> concepts with children: 2
#>
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family
#> number of concepts in level form: 0
#> number of concepts in level variety: 0
#> number of concepts in level subspecies: 0
#> number of concepts in level species: 1
#> number of concepts in level complex: 0
#> number of concepts in level genus: 1
#> number of concepts in level family: 1
#>
## Subset by taxon relations
Kenya_sub <- subset(
x = Kenya_veg, subset = Level == "species",
slot = "taxonRelations"
)
summary(Kenya_sub)
#> ## Metadata
#> db_name: Sweadataveg
#> sp_list: Easplist
#> dictionary: Swea
#> object size: 8657.9 Kb
#> validity: TRUE
#>
#> ## Content
#> number of plots: 1946
#> plots with records: 1946
#> variables in header: 34
#> number of relations: 3
#>
#> ## Taxonomic List
#> taxon names: 2089
#> taxon concepts: 1422
#> validity: TRUE
#>
summary(Kenya_sub@species)
#> object size: 353 Kb
#> validation of 'taxlist' object: TRUE
#>
#> number of taxon usage names: 2089
#> number of taxon concepts: 1422
#> trait entries: 102
#> number of trait variables: 1
#> taxon views: 3
#>
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family
#> number of concepts in level form: 0
#> number of concepts in level variety: 0
#> number of concepts in level subspecies: 0
#> number of concepts in level species: 1422
#> number of concepts in level complex: 0
#> number of concepts in level genus: 0
#> number of concepts in level family: 0
#>
## Subset by taxon traits
Kenya_sub <- subset(
x = Kenya_veg, subset = lf_behn_2018 == "obligate_annual",
slot = "taxonTraits"
)
summary(Kenya_sub)
#> ## Metadata
#> db_name: Sweadataveg
#> sp_list: Easplist
#> dictionary: Swea
#> object size: 965.9 Kb
#> validity: TRUE
#>
#> ## Content
#> number of plots: 1946
#> plots with records: 907
#> variables in header: 34
#> number of relations: 3
#>
#> ## Taxonomic List
#> taxon names: 121
#> taxon concepts: 32
#> validity: TRUE
#>
summary(Kenya_sub@species)
#> object size: 26.8 Kb
#> validation of 'taxlist' object: TRUE
#>
#> number of taxon usage names: 121
#> number of taxon concepts: 32
#> trait entries: 32
#> number of trait variables: 1
#> taxon views: 3
#>
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family
#> number of concepts in level form: 0
#> number of concepts in level variety: 0
#> number of concepts in level subspecies: 0
#> number of concepts in level species: 32
#> number of concepts in level complex: 0
#> number of concepts in level genus: 0
#> number of concepts in level family: 0
#>
## Subset by header
Kenya_sub <- subset(x = Kenya_veg, subset = ALTITUDE <= 1000, slot = "header")
summary(Kenya_sub)
#> ## Metadata
#> db_name: Sweadataveg
#> sp_list: Easplist
#> dictionary: Swea
#> object size: 725.2 Kb
#> validity: TRUE
#>
#> ## Content
#> number of plots: 16
#> plots with records: 16
#> variables in header: 27
#> number of relations: 3
#>
#> ## Taxonomic List
#> taxon names: 3164
#> taxon concepts: 2392
#> validity: TRUE
#>
## Subset by samples (after converting coverage)
Kenya_veg <- cover_trans(x = Kenya_veg, to = "cover_percentage", rule = "middle")
Kenya_sub <- subset(x = Kenya_veg, subset = cover_percentage >= 50, slot = "samples")
summary(Kenya_sub)
#> ## Metadata
#> db_name: Sweadataveg
#> sp_list: Easplist
#> dictionary: Swea
#> object size: 1489.8 Kb
#> validity: TRUE
#>
#> ## Content
#> number of plots: 1946
#> plots with records: 1084
#> variables in header: 34
#> number of relations: 3
#>
#> ## Taxonomic List
#> taxon names: 3164
#> taxon concepts: 2392
#> validity: TRUE
#>
## Subset by relations
Kenya_sub <- subset(
x = Kenya_veg, subset = as.integer(YEAR) >= 2000,
slot = "relations", relation = "REFERENCE"
)
summary(Kenya_sub)
#> ## Metadata
#> db_name: Sweadataveg
#> sp_list: Easplist
#> dictionary: Swea
#> object size: 2674.5 Kb
#> validity: TRUE
#>
#> ## Content
#> number of plots: 318
#> plots with records: 318
#> variables in header: 30
#> number of relations: 3
#>
#> ## Taxonomic List
#> taxon names: 3164
#> taxon concepts: 2392
#> validity: TRUE
#>