combine {vegsoup} | R Documentation |
Combine two or more taxa by selecting scientific species names.
combine(x, y, z)
x |
|
y |
list. List elements should be named |
z |
list. List elements should be named |
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).
returns an object depending on the input class.
Roland Kaiser
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")