GiniSimpson: Functions to calculate the GiniSimpson index

In VHIRHepatiques/QSutils: Quasispecies Diversity

Functions to calculate the GiniSimpson index

Description

GiniSimpson calculates the unbiased estimator, GiniSimpsonVar computes Gini-Simpson asymp- totic variance, and GiniSimpsonMVUE calculates the minimum variance unbiased estimator of the Gini-Simpson index.

Usage

GiniSimpson(w)
GiniSimpsonMVUE(w)
GiniSimpsonVar(w)

Arguments

w	Vector of observed counts or frequencies.

Value

A value that corresponds to the Gini-Simpson diversity index.

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

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

# Gini-Simpson index.
GiniSimpson(nr)

# Gini-Simpson variance. 
GiniSimpsonVar(nr)

# MVUE Gini-Simpson index. 
GiniSimpsonMVUE(nr)

VHIRHepatiques/QSutils documentation built on April 27, 2024, 10:29 p.m.