Rao {QSutils} | R Documentation

## Functions to compute Rao’s entropy

### Description

Set of functions to estimate Rao’s functional entropy. `Rao` calculates the Rao entropy, `RaoVar` the variance of the Rao estimator, `RaoPow` the Rao entropy of order q, and `RaoPowProfile` the functional Rao entropy profile for the given set of exponents.

### Usage

    Rao(dst, w=NULL)
    RaoVar(dst,w=NULL)
    RaoPow(dst,q,w=NULL)
    RaoPowProfile(dst,w=NULL,q=NULL)

### Arguments

`dst` | A "dist" object, output of the DNA.dist function.
`w` | An optional numeric vector with the haplotype counts. When `w` is NULL the same weight is given to each haplotype.
`q` | Exponent. A single value for `Rao`, `RaoVar` and `RaoPow`. A vector of values for `RaoPowProfile`. The default value for `RaoPowProfile` is a set of exponents to obtain a smooth profile.

### Value

A single value for `Rao`, `RaoVar` and `RaoPow`. A vector of values for `RaoPowProfile` corresponding to each exponent in vector q.

### 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

`DNA.dist`, `ReadAmplSeqs`

### Examples

    # Load haplotype alignment with abundances.
    filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
    lst <- ReadAmplSeqs(filepath,type="DNA")
    # DNA pairwise distances.
    dst <- DNA.dist(lst$hseqs,model="N")

    Rao(dst,lst$nr)
    RaoVar(dst,lst$nr)
    RaoPow(dst,2,lst$nr)
    RaoPowProfile(dst,lst$nr,c(0:4,Inf))
    RaoPowProfile(dst,lst$nr)

[Package QSutils version 1.2.0 Index]