Produce a Cocktail classification

Classification of vegtable objects according to Cocktail algorithms.

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.

These functions are implemented for constructing or complementing shaker objects. Note that construction of those objects will always require a companion object, which is either an object of class taxlist or vegtable.

Usage

set_group(shaker, companion, group, ...)

# S4 method for shaker,taxlist,character
set_group(
  shaker,
  companion,
  group,
  group_id,
  authority = FALSE,
  enc_cont = "latin1",
  enc_gr = "utf8",
  ...
)

# S4 method for shaker,vegtable,character
set_group(shaker, companion, group, ...)

set_pseudo(shaker, companion, pseudo, ...)

# S4 method for shaker,taxlist,character
set_pseudo(
  shaker,
  companion,
  pseudo,
  pseudo_id,
  authority = FALSE,
  enc_cont = "latin1",
  enc_gr = "utf8",
  ...
)

# S4 method for shaker,vegtable,character
set_pseudo(shaker, companion, pseudo, ...)

set_formula(shaker, companion, formula, ...)

# S4 method for shaker,taxlist,character
set_formula(
  shaker,
  companion,
  formula,
  formula_id,
  authority = FALSE,
  enc_cont = "latin1",
  enc_gr = "utf8",
  ...
)

# S4 method for shaker,vegtable,character
set_formula(shaker, companion, formula, ...)

make_cocktail(shaker, vegtable, ...)

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

Arguments

shaker: An object of class shaker containing the respective cocktail definitions.
companion: Either a taxlist or a vegtable object.
...: Further arguments passes from or to other methods.
authority: Logical value indicating whether author names should be included in the taxon name or not.
enc_cont, enc_gr: Encodings used for special characters.
pseudo, group: Character vector with names of taxa included in a pseudo-species or a species group.
pseudo_id, group_id, formula_id: Character value as name of the pseudo-species, species group or defined vegetation unit.
formula: Character vector including a formula as definition of a vegetation unit.
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.
in_header: Logical value indicating whether results of Cocktail classification should be inserted to the header of the input vegtable or not. In the second case, a data frame is provided as output.

Value

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

A shaker object.

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.

Kočí M, Chytrý M, Tichý 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.

Author

Miguel Alvarez kamapu78@gmail.com

Examples

## Example from Alvarez (2017)
Wetlands_veg <- make_cocktail(Wetlands, Wetlands_veg, cover = "percen")
summary(as.factor(Wetlands_veg@header$Syntax))
#>    +  HE1  HE2  HE3  HE4  HE5  HE6  HE7  HY1  HY2 NA's 
#>    1   10   10   10    6    8    4    2   10    8   31 

## Same but only for two vegetation units
Wetlands_veg <- make_cocktail(Wetlands, Wetlands_veg,
  which = c("HY1", "HY2"), cover = "percen"
)
summary(as.factor(Wetlands_veg$Syntax))
#>  HY1  HY2 NA's 
#>   10    8   82 

## Construct the 'shaker' object anew
Wetlands <- new("shaker")

## Set a pseudo-species
Wetlands <- set_pseudo(Wetlands, Wetlands_veg, c(
  "Cyperus latifolius",
  "Cyperus exaltatus"
))

## Set a species group
Wetlands <- set_group(Wetlands, Wetlands_veg,
  group_id = "Cyperus papyrus",
  group = c(
    "Cyperus papyrus",
    "Cyclosorus interruptus",
    "Lepistemon owariense"
  )
)

## Set a fromula
Wetlands <- set_formula(Wetlands, Wetlands_veg,
  formula_id = "HE1",
  formula = "groups:'Cyperus papyrus' | species:'Cyperus papyrus > 50'"
)

## Summaries
summary(Wetlands)
#> Number of pseudo-species: 1 
#> Number of species groups: 1 
#> Number of formulas: 1 
summary(Wetlands, Wetlands_veg)
#> ## Pseudo-species: 
#> * 'Cyperus latifolius' contains: 
#>      Cyperus exaltatus 
#> 
#> ## Species groups: 
#> * 'Cyperus papyrus' group: 
#>      Cyperus papyrus 
#>      Cyclosorus interruptus 
#>      Lepistemon owariense 
#> 
#> ## Formulas: 
#> * HE1: groups:'Cyperus papyrus' | species:'Cyperus papyrus > 50' 
#>