iNEXT: ChaoShannon – R documentation

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ChaoShannon

Estimation of Shannon entropy/diversity

Description

ChaoShannon: estimation of Shannon entropy or transformed Shannon diversity based on the method proposed by Chao et al. (2013)

Usage

ChaoShannon(x, datatype = "abundance", transform = FALSE,
  conf = 0.95, B = 200)

ChaoEntropy(x, datatype = "abundance", transform = FALSE,
  conf = 0.95, B = 200)

Arguments

`x`	a vector of species abundances or incidence frequencies. If `datatype = "incidence"`, then the first entry of the input data must be total number of sampling units, followed by species incidence frequencies.
`datatype`	data type of input data: individual-based abundance data (`datatype = "abundance"`), sampling-unit-based incidence frequencies data (`datatype = "incidence_freq"`) or species by sampling-units incidence matrix (`datatype = "incidence_raw"`).
`transform`	a `logical` constant to compute traditional Shannon entropy index (`transform=FALSE`) or the transformed Shannon diversity (`transform=TRUE`).
`conf`	a positive number ≤ 1 specifying the level of confidence interval.
`B`	an integer specifying the number of bootstrap replications.

Value

A vector of observed Shannon entropy/diversity, estimate of entropy/diversity, s.e. and the associated confidence interval.

References

Chao, A., Wang, Y.T. & Jost, L. (2013) Entropy and the species accumulation curve: a novel entropy estimator via discovery rates of new species. Methods in Ecology and Evolution, 4, 1091-1100.

Examples

data(spider)
ChaoShannon(spider$Girdled, datatype="abundance")

iNEXT

Interpolation and Extrapolation for Species Diversity

v2.0.20

GPL (>= 3)

Authors

T. C. Hsieh, K. H. Ma and Anne Chao

Initial release