make_cocktail | R Documentation |
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.
set_group(shaker, companion, group, ...)
## S4 method for signature 'shaker,taxlist,character'
set_group(
shaker,
companion,
group,
group_id,
authority = FALSE,
enc_cont = "latin1",
enc_gr = "utf8",
...
)
## S4 method for signature 'shaker,vegtable,character'
set_group(shaker, companion, group, ...)
set_pseudo(shaker, companion, pseudo, ...)
## S4 method for signature 'shaker,taxlist,character'
set_pseudo(
shaker,
companion,
pseudo,
pseudo_id,
authority = FALSE,
enc_cont = "latin1",
enc_gr = "utf8",
...
)
## S4 method for signature 'shaker,vegtable,character'
set_pseudo(shaker, companion, pseudo, ...)
set_formula(shaker, companion, formula, ...)
## S4 method for signature 'shaker,taxlist,character'
set_formula(
shaker,
companion,
formula,
formula_id,
authority = FALSE,
enc_cont = "latin1",
enc_gr = "utf8",
...
)
## S4 method for signature 'shaker,vegtable,character'
set_formula(shaker, companion, formula, ...)
make_cocktail(shaker, vegtable, ...)
## S4 method for signature 'shaker,vegtable'
make_cocktail(
shaker,
vegtable,
which,
cover,
syntax = "Syntax",
FUN = sum,
in_header = TRUE,
...
)
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 |
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. |
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.
Miguel Alvarez kamapu78@gmail.com
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.
shaker vegtable Wetlands
## Example from Alvarez (2017)
Wetlands_veg <- make_cocktail(Wetlands, Wetlands_veg, cover = "percen")
summary(as.factor(Wetlands_veg@header$Syntax))
## Same but only for two vegetation units
Wetlands_veg <- make_cocktail(Wetlands, Wetlands_veg,
which = c("HY1", "HY2"), cover = "percen"
)
summary(as.factor(Wetlands_veg$Syntax))
## 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)
summary(Wetlands, Wetlands_veg)
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