KinMixLite-package {KinMixLite}

Inference About Relationships from DNA Mixtures

Description

Methods for inference about relationships between contributors to a DNA mixture and other individuals of known genotype: a basic example would be testing whether a contributor to a mixture is the father of a child of known genotype. This provides most of the functionality of the 'KinMix' package, but with some loss of efficiency and restriction on problem size, as the latter uses 'RHugin' as the Bayes net engine, while this package uses 'gRain'. The package implements the methods introduced in Green, P. J. and Mortera, J. (2017) <doi:10.1016/j.fsigen.2017.02.001> and Green, P. J. and Mortera, J. (2021) <doi:10.1111/rssc.12498>.

Details

This package is a toolkit for inference about mixtures and familial relationships, either between contributors or between a contributor and other typed individuals. It extends the functionality proposed in Green and Mortera (2017) by allowing more general relationships, specified in general by an IBD pattern distribution - the generalisation to more than two individuals of the coefficients of identity of Jacquard (1974). Details are in the paper by Green and Mortera (2021). KinMixLite extends the capability of the DNAmixturesLite package, and intimately relies on that package; as with that package, instead of the RHugin package, it uses gRaven and gRain for Bayes Net calculations. This version implements the ALN, MBN and WLR as well as RPT methods; see Green and Mortera (2017).

Formats

See formats for formats of the various data objects used in this package.

Author(s)

Maintainer: Peter Green <[e-mail]>

References

Green, P. J. and Mortera, J. (2017). Paternity testing and other inference about relationships from DNA mixtures. Forensic Science International: Genetics. <doi:10.1016/j.fsigen.2017.02.001>.

Green, P. J. and Mortera, J. (2021). Inference about complex relationships using peak height data from DNA mixtures. Applied Statistics. <doi:10.1111/rssc.12498>.

Jacquard, A. (1974) The genetic structure of populations. Springer-Verlag.

See Also

DNAmixturesLite

Examples

require(ribd)
data(test2data)
data(NGMDyes)

C<-50

## Fit 2-person mixture - baseline model

mixD<-DNAmixture(list(epg),k=2,C=list(C),database=db)
pars<-mixpar(rho=list(2),eta=list(100),xi=list(0.1),phi=list(c(U1=0.7,U2=0.3)))
baseline<-logL(mixD)(pars)

## Fit 2-person mixture model in which contributor 1 is parent of a typed individual Cgt

mixD<-DNAmixture(list(epg),k=2,C=list(C),database=db,triangulate=FALSE,compile=FALSE)
rpt.IBD(mixD,'parent',list(c=Cgt),targets=c('f','c'),contrib='f') 
log10LR<-(logL(mixD)(pars)-baseline)/log(10)
cat('log10 LR',log10LR,'\n')

## Fit 2-person mixture, where contributors are siblings

mixD<-DNAmixture(list(epg),k=2,C=list(C),database=db)
pars<-mixpar(rho=list(2),eta=list(100),xi=list(0.1),phi=list(c(U1=0.6,U2=0.3,U3=0.1)))
baseline<-logL(mixD)(pars)

mixD<-DNAmixture(list(epg),k=2,C=list(C),database=db,triangulate=FALSE,compile=FALSE)
rpt.IBD(mixD,'sibs',targets=c('b1','b2'),contribs=c('b1','b2')) 
log10LR<-(protected(logL(mixD)(pars))-baseline)/log(10)
cat('log10 LR',log10LR,'\n')