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msap (version 1.1.8)

shannon: Shannon Index of phenotypic diversity

Description

Calculate Shannon Index of phenotypic diversity given a list of binary alleles.

Usage

shannon(x)

Arguments

x
A list of binary values or alleles.

Value

The value of the Shannon Index of phenotypic diversity

Details

The Shannon index of phenotypic diversity, S, derived from the Shannon-Weaver index (Shannon, 1948): $$ S=-\sum_{i=1}^{n} p_{i}\log_{2}p_i $$

where $p_{i}$ is the frequency of the band presence at the ith marker within the population. This index gives more weight to the presence than to the absence of bands. This has no real biological support, although it might account for the occurrence of homoplasic absences of bands (Bonin et al., 2007)

References

Bonin, A., Ehrich, D. and Manel S. 2007. Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolucionists. Molecular Ecology 16, 3737-3758.

Shannon, C. E. 1948. A mathematical theory of comunication. Bell System Technical Journal 27, 379-423.