entropart (version 1.1.1)

GammaDiversity: Unbiased gamma diversity of a metacommunity

Description

Calculates the unbiased diversity of order $q$ of a metacommunity.

Usage

GammaDiversity(MC, q, Correction = "Best", Tree = NULL, Normalize = TRUE, 
  CheckArguments = TRUE)

Arguments

MC

A MetaCommunity object.

q

A number: the order of diversity.

Correction

A string containing one of the possible corrections: "ChaoShen", "Grassberger", "Holste", "Bonachela" or "Best", the default value.

Tree

An object of class hclust or phylog. The tree must be ultrametric.

Normalize

If TRUE (default), diversity is not affected by the height of the tree. If FALSE, diversity is proportional to the height of the tree.

CheckArguments

Logical; if TRUE, the function arguments are verified. Should be set to FALSE to save time when the arguments have been checked elsewhere.

Value

• The metacommunity's gamma entropy.

Details

Entropy is calculated by GammaEntropy and transformed into diversity.

References

Marcon, E., Scotti, I., Herault, B., Rossi, V. and Lang, G. (in revision). Generalization of the partitioning of Shannon diversity. PLOS One. Marcon, E., Herault, B. (in prep). Partitioning phylodiversity. Methods in Ecology and Evolution.

See Also

GammaEntropy

Examples

# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
  data(Paracou618)
  # Calculate Simpson gamma diversity
  GammaDiversity(Paracou618.MC, 2)
  # Compare without correction
  GammaDiversity(Paracou618.MC, 2, Correction = "None")
  # Estimate phylogenetic Simpson gamma diversity
  GammaDiversity(Paracou618.MC, 2, Tree = Paracou618.Taxonomy)