Reduced-bias beta diversity of a metacommunity

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Description

Calculates the reduced-bias beta diversity of order q between communities.

Usage

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BetaDiversity(MC, q = 1, Correction = "Best", Tree = NULL, Normalize = TRUE, 
  Z = NULL, CheckArguments = TRUE)

Arguments

MC

A MetaCommunity object.

q

A number: the order of diversity. Default is 1 for Shannon diversity.

Correction

A string containing one of the possible corrections accepted by bcTsallisBeta or "None" 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.

Z

A relatedness matrix, i.e. a square matrix whose terms are all positive, strictly positive on the diagonal. Generally, the matrix is a similarity matrix, i.e. the diagonal terms equal 1 and other terms are between 0 and 1.

CheckArguments

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

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).

Value

An MCdiversity object containing diversity value of the metacommunity.

Author(s)

Eric Marcon <Eric.Marcon@ecofog.gf>

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. (2015). Decomposing Phylodiversity. Methods in Ecology and Evolution 6(3): 333-339.

Marcon, E., Zhang, Z. and Herault, B. (2014). The decomposition of similarity-based diversity and its bias correction. HAL hal-00989454(version 1).

See Also

BetaEntropy

Examples

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  # 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)

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