Renyi: Rényi profiles

In VHIRHepatiques/QSutils: Quasispecies Diversity

Rényi profiles

Description

Functions to compute the Rényi entropy given a vector of counts RenyiProfile computes the Rényi number for a set of exponents.

Usage

Renyi(w, q)
RenyiProfile(w, q = NULL)

Arguments

w	Vector of observed counts or frequencies.
q	Exponent. A single value for Renyi, a vector of values or NULL for RenyiProfile.

Value

A single value for Renyi. A data frame with exponents and entropies for RenyiProfile.

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.

Pavoine, S. (2005). Méthodes statistiques pour la mesure de la biodiversité. UMR CNRS 5558 «Biométrie et Biologie Evolutive».

See Also

Hill, HCq

Examples

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

Renyi(nr,2)

RenyiProfile(nr,c(0:4,Inf))

RenyiProfile(nr)

VHIRHepatiques/QSutils documentation built on April 12, 2024, 12:25 p.m.