vegtable (version 0.1.3)

make_cocktail: Produce a Cocktail classification.

Description

Classification of '>vegtable objects according to Cocktail algorithms.

Usage

# S4 method for shaker,vegtable
make_cocktail(shaker, vegtable, which, cover,
	syntax="Syntax", FUN=sum, ...)

Arguments

shaker

An object of class '>shaker containing the respective cocktail definitions.

vegtable

An object of class '>vegtable containing the vegetation observations to be classified.

which

Integer or character indicating the definition to be applied for classification.

cover

Name of the cover variable in vegtable.

syntax

Character value indicating the name of the retrieved variable including the final classification of plots.

FUN

Function used for merging multiple occurrence of species in a single plot.

...

Further arguments passed from or to other methods.

Value

A data frame corresponding to the slot 'header' of input object 'vegtable', including the results of Cocktail classification for the respective plots.

Details

Cocktail algorithms are logical functions selecting plots according to either occurrence of species groups and cover values of single species. A group will be declared as occurring in a plot when at least a half of its members is present in the plot.

This function inserts single columns with logical values indicating whether a plot is classified in the vegetation unit or not. An additional column (name provided in argument 'syntax') compile all vegetation units, indicating with a '+' symbol those plots classified in more than one vegetation unit. When only a part of the formulas will be used, it should be specified by the argument 'which'.

References

Alvarez M (2017). Classification of aquatic and semi-aquatic vegetation in two East African sites: Cocktail definitions and syntaxonomy. Phytocoenologia.

Bruelheide H (2000). A new measure of fidelity and its application to defining species groups. Journal of Vegetation Science 11: 167--178.

Ko<U+010D><U+00ED> M, Chytr<U+00FD> M, Tich<U+00FD> L (2003). Formalized reproduction of an expert-based phytosociological classification: a case study of subalpine tall-forb vegetation. Journal of Vegetation Science 14: 601--610.

See Also

'>shaker, '>vegtable, Wetlands.

Examples

# NOT RUN {
library(vegtable)

## Example from Alvarez (2017)
data(Wetlands)

Wetlands_veg@header <- make_cocktail(Wetlands, Wetlands_veg, cover="percen")
summary(as.factor(Wetlands_veg@header$Syntax))

## Same but only for two vegetation units
data(Wetlands)
Wetlands_veg@header <- make_cocktail(Wetlands, Wetlands_veg,
	which=c("HY1","HY2"), cover="percen")
summary(as.factor(Wetlands_veg@header$Syntax))
# }