combine: Combine taxa

In vegsoup: Classes and Methods for Phytosociology

Description

Combine two or more taxa by selecting scientific species names.

Usage

combine(x, y, z)

Arguments

x	Vegsoup* object.
y	list. List elements should be named from and to. Entries must not to be named, but should otherwise be in that order.
z	list. List elements should be named abbr and taxon, as in taxonomy(x). Entries must not to be named, see above.

Details

This utility function can be used to perform taxonomic aggregation. Argument y defines the taxa to be combined (list element from) and a new taxonomic description of that aggregation (list element to). Argument z holds the new abbreviation (see class Taxonomy) for the aggregated taxon and a taxonomic description of that aggregation (cp. argument y). Element z can also be missing. In this case y$to is queried from taxonomy(x). This is the case if a lower level taxon (a subspecies) is combined with the higher level nominat form (s.lat., Genus species ssp. subspecies = Genus species s.lat.). Note, if any z$abbr or z$taxon equals an exiting entry in taxonomy(x) it has to be quoted in y$from (see ‘Examples’, for Scapania).

Value

returns an object depending on the input class.

Author(s)

Roland Kaiser

See Also

layers

Examples

require(vegsoup)

data(barmstein)
x <- barmstein

# display all taxa
taxon(x)

# pool to a new add-hoc taxon 
y <- list(from = c("Teucrium chamaedrys ssp. chamaedrys", "Teucrium montanum"),
          to = "Teucrium chamaedrys/montanum")
z <- list(abbr = "teuc cham mont",
          taxon = "Teucrium chamaedrys/montanum")

# display taxa again
taxon(combine(x, y, z))

data(windsfeld)
x <- windsfeld

# pooling taxa with an existing taxon
taxon(x, "Scapania")
y <- list(from = c("Scapania aequiloba", "Scapania aspera",
          "Scapania curta agg."),
          to = "Scapania curta agg.")
z <- list(abbr = "scap curt aggr",
          taxon = y$to)
taxon(combine(x, y, z), "Scapania")

# we can omit z if y$to exists in the data set
taxon(x, "Biscutella")
y <- list(from = c("Biscutella laevigata ssp. laevigata"),
          to = "Biscutella laevigata s.lat.")
taxon(combine(x, y), "Biscutella")

vegsoup documentation built on Feb. 24, 2021, 3 a.m.