Hill: Hill numbers

In VHIRHepatiques/QSutils: Quasispecies Diversity

Hill numbers

Description

Functions to compute Hill numbers. Hill computes the Hill number of a single q value. HillProfile computes Hill numbers for all elements in vector q.

Usage

Hill(w, q)
HillProfile(w, q = NULL)

Arguments

w	Vector of observed counts or frequencies.
q	Exponent.

Details

In Hill , only the first element in q is considered. HillProfile is vectorized and considers all elements in q.When q is NULL: in this case, a default vector is taken to obtain the full profile in the range, 0 to Inf.

Value

A value or vector of values corresponding to the Hill number estimators of passed exponents.

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.

See Also

HCq, Renyi

Examples

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

# Hill numbers of order 2.
Hill(nr,2)

# Set of most common values.
HillProfile(nr,q=c(0:4,Inf))

# Full Hill numbers profile.
HillProfile(nr)

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