BetaEntropy {entropart}R Documentation

Reduced-bias beta entropy of a metacommunity


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


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



A MetaCommunity object.


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


A string containing one of the possible corrections accepted by the bias-corrected entropy function (see details) or "None" or "Best", the default value.


An object of class hclust, phylo, phylog or PPtree. The tree must be ultrametric.


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.


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.


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


If Tree is not NULL, then phylogenetic entropy is calculated by bcPhyloBetaEntropy; else, if Z is not NULL, then similarity-based entropy is calculated by bcHqzBeta; else, neutral entropy is calculated by bcTsallisBeta.

The reduced-bias 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.


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


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

bcTsallisBeta, BetaDiversity


# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
# 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)

[Package entropart version 1.6-13 Index]