Abundance Frequency Count of a Community

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Description

Counts the number of species observed the same number of times.

Usage

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AbdFreqCount(Ns, CheckArguments = TRUE)

Arguments

Ns

A numeric vector containing species abundances.

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 Abundance Frequency Count (Chao et al., 2015) is the number of species observed each number of times.

It is a way to summarize the species distribution.

Value

A two-column matrix. The first column contains the number of observations, the second one the number of species observed this number of times.

Author(s)

Eric Marcon <Eric.Marcon@ecofog.gf>

References

Chao, A., Hsieh, T. C., Chazdon, R. L., Colwell, R. K., Gotelli, N. J. (2015) Unveiling the Species-Rank Abundance Distribution by Generalizing Good-Turing Sample Coverage Theory. Ecology 96(5): 1189-1201.

See Also

PhyloEntropy, ChaoPD

Examples

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  # Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest
  #      and their taxonomy)
  data(Paracou618)
  # Ns is the vector of abundances of the first plot
  Ns <- Paracou618.MC$Nsi[, 1]
  
  # Return the abundance frequency count
  (AbdFreqCount(Ns) -> afc)
  plot(afc, xlab="Number of observations", ylab="Number of species")
  lines(afc)

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