GammaEntropy {entropart} | R Documentation |
Calculates the reduced-bias Tsallis entropy of order q
of a metacommunity.
GammaEntropy(MC, q = 1, Correction = "Best", Tree = NULL, Normalize = TRUE,
Z = NULL, PhyloDetails = FALSE, CheckArguments = TRUE)
MC |
A |
q |
A number: the order of entropy. Default is 1. |
Correction |
A string containing one of the possible corrections accepted by the bias-corrected entropy function (see details) or |
Tree |
An object of class |
Normalize |
If |
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. |
PhyloDetails |
If |
CheckArguments |
Logical; if |
If Tree
is not NULL
, then phylogenetic entropy is calculated by bcPhyloEntropy
.
Else, if Z
is not NULL
, then similarity-based entropy is calculated by bcHqz
.
Else, neutral entropy is calculated by bcTsallis
.
A number equal to the calculated entropy.
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).
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
data(Paracou618)
# Calculate Simpson gamma entropy
GammaEntropy(Paracou618.MC, 2)
# Compare without correction
GammaEntropy(Paracou618.MC, 2, Correction = "None")
# Estimate phylogenetic Simpson gamma entropy
GammaEntropy(Paracou618.MC, 2, Tree = Paracou618.Taxonomy)