Simpson beta entropy of a community

Description

Calculates the Simpson beta entropy of a community belonging to a metacommunity.

Usage

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SimpsonBeta(NorP, NorPexp = NULL, Correction = "Best", CheckArguments = TRUE, 
  Ps = NULL, Ns = NULL, Pexp = NULL, Nexp = NULL)
bcSimpsonBeta(Ns, Nexp, Correction = "Best", CheckArguments = TRUE)
## S3 method for class 'ProbaVector'
SimpsonBeta(NorP, NorPexp = NULL, Correction = "Best", CheckArguments = TRUE, 
  Ps = NULL, Ns = NULL, Pexp = NULL, Nexp = NULL)
## S3 method for class 'AbdVector'
SimpsonBeta(NorP, NorPexp = NULL, Correction = "Best", CheckArguments = TRUE, 
  Ps = NULL, Ns = NULL, Pexp = NULL, Nexp = NULL)
## S3 method for class 'integer'
SimpsonBeta(NorP, NorPexp = NULL, Correction = "Best", CheckArguments = TRUE, 
  Ps = NULL, Ns = NULL, Pexp = NULL, Nexp = NULL)
## S3 method for class 'numeric'
SimpsonBeta(NorP, NorPexp = NULL, 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.

Correction

A string containing one of the possible corrections: currently, only "ChaoShen", identical to "Best".

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

The derivation of Tsallis beta entropy (Simpson is Tsallis of order 2) can be found in Marcon et al. (2014).

Bias correction requires the number of individuals to estimate sample Coverage. Use bcSimpsonBeta and choose the Correction.

Note that Simpson beta entropy value is related to Simpson alpha entropy value and cannot be compared accross communities (Jost, 2007). Beta entropy of a community is not meaningful in general, do rather calculate the BetaDiversity of order 2 of the metacommunity.

The functions are designed to be used as simply as possible. SimpsonBeta 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 bcSimpsonBeta is called. Explicit calls to bcSimpsonBeta (with bias correction) or to SimpsonBeta.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.

Author(s)

Eric Marcon <Eric.Marcon@ecofog.gf>

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.

See Also

Simpson, bcSimpsonBeta, BetaDiversity

Examples

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  # 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 <- as.ProbaVector(Paracou618.MC$Ps)
  # Probability distribution of the first plot
  Ps1 <- as.ProbaVector(Paracou618.MC$Psi[, 1])

  # Simpson beta entropy of the plot
  SimpsonBeta(Ps1, Ps)
  # Transform into diversity
  expq(SimpsonBeta(Ps1, Ps)/(1-Simpson(Ps1)), 2)
  
  # Ns is the vector of abundances of the metacommunity
  Ns <- as.AbdVector(Paracou618.MC$Ns)
  # Abundances in the first plot
  Ns1 <- as.AbdVector(Paracou618.MC$Nsi[, 1])
  # Reduced-bias Shannon beta entropy of the plot
  bcSimpsonBeta(Ns1, Ns)

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