Shannon: Set of functions to compute Shannon entropy

In QSutils: Quasispecies Diversity

Description

Shannon computes the Shannon entropy. NormShannon returns the normalized Shannon entropy. ShannonVar computes the Shannon entropy asymptotic variance. NormShannonVar computes the normalized Shannon entropy asymptotic variance.

Usage

Shannon(w)
ShannonVar(w)
NormShannon(w)
NormShannonVar(w)

Arguments

w	Vector of observed counts or frequencies.

Value

A single value with the result of the computations.

Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

References

Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.

Gregori J, Salicrú M, Domingo E, Sanchez A, Esteban JI, Rodríguez-Frías F, Quer J. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics. 2014 Apr 15;30(8):1104-1111. Epub 2014 Jan 2. PubMed PMID: 24389655.

Examples

# Create a vector of observed counts.
nr<-c(464, 62, 39, 27, 37, 16, 33, 54, 248, 20)

# Shannon entropy.
Shannon(nr)

# Shannon entropy variance.
ShannonVar(nr)

# Normalized Shannon entropy.
NormShannon(nr)

# Normalized Shannon entropy variance.
NormShannonVar(nr)

QSutils documentation built on Nov. 8, 2020, 7:42 p.m.