entropart (version 1.1.3)

BetaDiversity: Unbiased beta diversity of a metacommunity

Description

Calculates the unbiased beta diversity of order $q$ between communities.

Usage

BetaDiversity(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 accepted by bcTsallisBeta. "Best" is 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 value of the metacommunity.

Details

Entropy is calculated by BetaEntropy and transformed into diversity. Diversity values of communities are not defined: community entropies are averaged to obtain the metacommunity entropy wich is transformed into diversity (Marcon et al., 2014).

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

BetaEntropy

Examples

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