ChaoShannon
: estimation of Shannon entropy or transformed Shannon diversity based on the method proposed by Chao et al. (2013)
ChaoShannon(x, datatype = "abundance", transform = FALSE, conf = 0.95, B = 200)
A data.frame of observed Shannon entropy/diversity, estimate of entropy/diversity, s.e. and the associated confidence interval.
a matrix
, data.frame
(species by sites), or list
of species abundances or incidence frequencies. If datatype = "incidence_freq"
,
then the first entry of the input data must be total number of sampling units, followed by species incidence frequencies.
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"
).
a logical
constant to compute traditional Shannon entropy index (transform=FALSE
) or the transformed Shannon diversity (transform=TRUE
).
a positive number \(\le\) 1 specifying the level of confidence interval.
an integer specifying the number of bootstrap replications.
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.
ChaoRichness, ChaoSimpson
data(spider)
ChaoShannon(spider$Girdled, datatype="abundance")
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