HCDT diversity of a community

Description

Calculates the HCDT (generalized) diversity of order q of a probability vector.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
Diversity(NorP, q = 1, Correction = "Best", CheckArguments = TRUE, 
  Ps = NULL, Ns = NULL)
bcDiversity(Ns, q = 1, Correction = "Best", CheckArguments = TRUE)
## S3 method for class 'ProbaVector'
Diversity(NorP, q = 1, Correction = "Best", CheckArguments = TRUE, 
  Ps = NULL, Ns = NULL)
## S3 method for class 'AbdVector'
Diversity(NorP, q = 1, Correction = "Best", CheckArguments = TRUE, 
  Ps = NULL, Ns = NULL)
## S3 method for class 'integer'
Diversity(NorP, q = 1, Correction = "Best", CheckArguments = TRUE, 
  Ps = NULL, Ns = NULL)
## S3 method for class 'numeric'
Diversity(NorP, q = 1, Correction = "Best", 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.

q

A number: the order of diversity. Default is 1.

Correction

A string containing one of the possible corrections: "None" (no correction), "ChaoShen", "GenCov", "Grassberger", "Holste", "Bonachela", "ZhangGrabchak", or "ChaoWangJost", "Marcon", "UnveilC", "UnveiliC", "UnveilJ" or "Best", the default value. Currently, "Best" is "ChaoWangJost".

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

Diversity calls Tsallis to calculate entropy and transforms it into diversity by calculating its deformed exponential.

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

The functions are designed to be used as simply as possible. Diversity 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 bcDiversity is called. Explicit calls to bcDiversity (with bias correction) or to Diversity.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 diversity. The name is that of the bias correction used.

Author(s)

Eric Marcon <Eric.Marcon@ecofog.gf>

References

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

Tsallis, expq, AbdVector, ProbaVector

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
  # 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)
  # Whittaker plot
  plot(Ns)
  # Calculate diversity of order 1, i.e. Shannon's diversity
  Diversity(Ps, 1)
  # Calculate it with estimation bias correction
  Diversity(Ns, 1)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.