entropart (version 1.1.3)

AlphaDiversity: Unbiased alpha diversity of a metacommunity

Description

Calculates the unbiased total alpha diversity of order $q$ of communities.

Usage

AlphaDiversity(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

• An MCdiversity object containing diversity values of each community and of the metacommunity.

Details

Entropy is calculated by AlphaEntropy and transformed into diversity.

References

Marcon, E., Scotti, I., Herault, B., Rossi, V. and Lang, G. (2014). Generalization of the partitioning of Shannon diversity. PLOS One 9(3): e90289. Marcon, E., Herault, B. (2014). Decomposing Phylodiversity. HAL hal-00946177(version 1).

See Also

AlphaEntropy

Examples

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