entropart (version 1.4-8)

AlphaDiversity: Reduced-bias alpha diversity of a metacommunity

Description

Calculates the eeduced-bias total alpha diversity of order \(q\) of communities.

Usage

AlphaDiversity(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 AlphaEntropy or "None" or "Best", the default value.

Tree

An object of class hclust, phylo, phylog or PPtree. 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.

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. (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 3).

See Also

AlphaEntropy

Examples

# NOT RUN {
  # 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)  
# }