entropart (version 1.1.3)

BetaEntropy: Unbiased beta entropy of a metacommunity

Description

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

Usage

BetaEntropy(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), the entropy returned by the function is normalized by the height of the tree (it is the weighted average value of the entropy in each slice). If FALSE, it is the unnormalized weighted sum of the results.

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 MCentropy object containing entropy values of each community and of the metacommunity.

Details

If Tree is NULL, then generalized entropy is calculated by bcTsallisBeta, else phylogenetic entropy is calculated by bcPhyloBetaEntropy. The unbiased beta entropy of each community is calculated and summed according to community weights. Note that beta entropy is related to alpha entropy (if $q$ is not 1) and cannot be compared accross communities (Jost, 2007). Do rather calculate the BetaDiversity of the metacommunity.

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.

See Also

bcTsallisBeta, BetaDiversity

Examples

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