Rao Quadratic Entropy of a Community

Calculates Rao's quadratic entropy of a community described by a probability vector and a phylogenetic / functional tree.

Usage

Rao(NorP, Tree, ...)
bcRao(Ns, Tree, Correction="Lande", CheckArguments = TRUE)
# S3 method for class 'ProbaVector'
Rao(NorP, Tree, ..., CheckArguments = TRUE, Ps = NULL)
# S3 method for class 'AbdVector'
Rao(NorP, Tree, Correction = "Lande", ..., 
  CheckArguments = TRUE, Ns = NULL)
# S3 method for class 'integer'
Rao(NorP, Tree, Correction = "Lande", ..., 
  CheckArguments = TRUE, Ns = NULL)
# S3 method for class 'numeric'
Rao(NorP, Tree, Correction = "Lande", ..., 
  CheckArguments = TRUE, Ps = NULL, Ns = NULL)

Arguments

Ps: A probability vector, summing to 1.
Ns: A numeric vector containing species abundances.
NorP: A numeric vector, an integer vector, an abundance vector (AbdVector) or a probability vector (ProbaVector). Contains either abundances or probabilities.
Tree: An object of class hclust, "phylo" (see read.tree), phylog or PPtree. The tree must be ultrametric.
Correction: A string containing one of the possible corrections accepted by bcTsallis or "Lande", the default value (equivalent to "Best").
...: Additional arguments. Unused.
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

Bias correction requires the number of individuals. Use bcRao and choose the Correction.

The unbiased estimator of Rao's entropy is identical to that of Simpson's entropy because Rao's entropy is a linear sum of Simson entropies, all of them calculated from the same number of individuals (Marcon and Herault, 2014). It equals the plug-in etimator multiplied by n/(n-1) where n is the total number of individuals.

The functions are designed to be used as simply as possible. Tsallis is a generic method. If its first argument is an abundance vector, an integer vector or a numeric vector which does not sum to 1, the bias corrected function bcTsallis is called. Explicit calls to bcTsallis (with bias correction) or to Tsallis.ProbaVector (without correction) are possible to avoid ambiguity. The .integer and .numeric methods accept Ps or Ns arguments instead of NorP for backward compatibility.

Value

A named number equal to the calculated entropy. The name is that of the bias correction used.

References

Marcon, E., Herault, B. (2015). Decomposing Phylodiversity. Methods in Ecology and Evolution 6(3): 333-339.

Rao, C. R. (1982). Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology 21: 24-43.

Examples

# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
data(Paracou618)
# Ns is the total number of trees per species
Ns <- as.AbdVector(Paracou618.MC$Ns)
# Species probabilities
Ps <- as.ProbaVector(Paracou618.MC$Ns)
# Calculate Rao's quadratic entropy of the plot
Rao(Ps, Paracou618.Taxonomy)
#>     None 
#> 2.878133