entropart (version 1.4-6)

TsallisBeta: Tsallis beta entropy of a community

Description

Calculates the Tsallis beta entropy of order $q$ of a community belonging to a metacommunity.

Usage

TsallisBeta(NorP, NorPexp = NULL, q = 1, Correction = "Best", CheckArguments = TRUE,  Ps = NULL, Ns = NULL, Pexp = NULL, Nexp = NULL)
bcTsallisBeta(Ns, Nexp = NULL, q, Correction = "Best", CheckArguments = TRUE)
"TsallisBeta"(NorP, NorPexp = NULL, q = 1, Correction = "Best", CheckArguments = TRUE,  Ps = NULL, Ns = NULL, Pexp = NULL, Nexp = NULL)
"TsallisBeta"(NorP, NorPexp = NULL, q = 1, Correction = "Best", CheckArguments = TRUE,  Ps = NULL, Ns = NULL, Pexp = NULL, Nexp = NULL)
"TsallisBeta"(NorP, NorPexp = NULL, q = 1, Correction = "Best", CheckArguments = TRUE,  Ps = NULL, Ns = NULL, Pexp = NULL, Nexp = NULL)
"TsallisBeta"(NorP, NorPexp = NULL, q = 1, Correction = "Best", CheckArguments = TRUE,  Ps = NULL, Ns = NULL, Pexp = NULL, Nexp = NULL)

Arguments

Ps

The probability vector of species of the community.

Pexp

The probability vector of species of the metacommunity.

Ns

A numeric vector containing species abundances of the community.

Nexp

A numeric vector containing species abundances of the metacommunity.

NorP

A numeric vector, an integer vector, an abundance vector (AbdVector) or a probability vector (ProbaVector). Contains either abundances or probabilities of the community.

NorPexp

A numeric vector, an integer vector, an abundance vector (AbdVector) or a probability vector (ProbaVector). Contains either abundances or probabilities of the metacommunity.

q

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

Correction

A string containing one of the possible corrections: currently, only "ChaoShen" or "None". "Best" is the default value, it is equivalent to "ChaoShen".

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

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

Details

The derivation of Tsallis beta entropy can be found in Marcon et al. (2014). Bias correction requires the number of individuals to estimate sample Coverage. Use bcTsallisBeta and choose the Correction.

Note that beta entropy value is related to alpha entropy (if $q$ is not 1) and cannot be compared accross communities (Jost, 2007). Beta entropy of a community is not meaningful in general, do rather calculate the BetaDiversity of the metacommunity.

The functions are designed to be used as simply as possible. TsallisBeta 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 bcTsallisBeta is called. Explicit calls to bcTsallisBeta (with bias correction) or to TsallisBeta.ProbaVector (without correction) are possible to avoid ambiguity. The .integer and .numeric methods accept Ps or Ns arguments instead of NorP for backward compatibility.

References

Jost (2007), Partitioning diversity into independent alpha and beta components. Ecology 88(10): 2427-2439.

Marcon, E., Scotti, I., Herault, B., Rossi, V. and Lang, G. (2014). Generalization of the partitioning of Shannon diversity. PLOS One 9(3): e90289.

Examples

  # Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
  data(Paracou618)
  # Ps is the vector of probabilities
  Ps <- Paracou618.MC$Ps
  # Probability distribution of the first plot
  Ps1 <- Paracou618.MC$Psi[, 1]
  # Divergence of order 2 between plot 1 and the whole forest
  TsallisBeta(Ps1, Ps, 2)

  # Ns is the vector of abundances of the metacommunity
  Ns <- Paracou618.MC$Ns
  # Abundances in the first plot
  Ns1 <- Paracou618.MC$Nsi[, 1]
  # Divergence of order 2 between plot 1 and the whole forest, with bias correction
  bcTsallisBeta(Ns1, Ns, 2)