simLR: Likelihood for mixtures that may have related contributors...
In euroMixR: Calculations for DNA mixtures, only R code

Description Usage Arguments Value Author(s) See Also Examples

Likelihood for mixtures that may have related contributors and drop-in and drop-out of alleles. For a general description of the problem, see see paraMix. As opposed to paraMix, drop-in and drop-out of alleles are allowed. The likelihood is based on simulations from an urn model. Possible mixtures are simulated by applying drop-in and drop-out to genotypes for the assumed contributors. Genotypes for unknown contributors are simulated conditioned on the pedigree.

1	simLR(R, x, alleles, afreq, pDO, pDI, N, known_genotypes = NULL, ped = NULL, id.U = NULL, id.V = NULL)

`R`	Integers, mixture
`x`	Number of unknown contributors
`alleles`	Integers indicating alleles for marker
`afreq`	A numerical vector with allele frequencies
`pDO`	Probability of drop-out applied per allele
`pDI`	Probability of drop-in per locus
`N`	Number of simulations
`known_genotypes`	List of known genotypes. If a pedigree is specified, each element must a triplet of integers corresponding to (id,allele1,allele2). If no pedigree is specified, the id can be omitted.
`ped`	`linkdat` object, or a list of such (if disconnected), describing the claimed relationship.
`id.U`	Integers indicating untyped contributors (e.g.,suspect(s)). Only relevant if a pedigree is specified.
`id.V`	Integers indicating typed non-contributors. Only relevant if a pedigree is specified.

p.R: the likelihood of the mixture R

Guro Dorum and Thore Egeland <guro.dorum@umb.no>

See paraMix.

require(paramlink)
alleles <-1:4
p <- c(0.044, 0.166, 0.11, 0.68)
names(p) <- alleles
R <- 1:3
known <- list(c(6,1,2),c(4,3,3))
x <- halfCousinPed(0)
y <- singleton(6,sex=2)
pDO <- 0.1
pDI <- 0.05
N <- 20000
lp <- simLR(R=R, x=0, alleles=alleles, afreq=p, pDO, pDI, N, known_genotypes=known, ped=list(x,y))
ld <- simLR(R=R, x=1, alleles=alleles, afreq=p, pDO, pDI, N, known_genotypes=known, ped=list(x,y), id.U=5,id.V=4)
lp/ld