likJ: Likelihood for two Possibly Inbred Individuals as a function...

In thoree/inbred: Different functions related to LR, bootstrap etc

Description

Likelihood for two Possibly Inbred Individuals as a function of the Condensed 'Jacquard' Coefficients

Usage

likJ(a, b, cc, d, pa, pb, pc, pd, Delta)

Arguments

a	Vector of positive integers (allele 1 of individual 1)
b	Vector of positive integers (allele 2 of individual 1)
cc	Vector of positive integers (allele 1 of individual 2)
d	Vector of positive integers (allele 2 of individual 2)
pa	Double vector of allele frequencies
pb	Double vector of allele frequencies
pc	Double vector of allele frequencies
pd	Double vector of allele frequencies
Delta	Double vector of length 9 summing to unity

Examples

p = c("1" = 0.1, "2" = 0.9)
a  = c(rep(1,6), rep(2,3))
b  = c(rep(1,3), rep(2,6))
cc = rep(c(1,1,2), 3)
d  = rep(c(1,2,2), 3)
pa = p[a]
pb = p[b]
pc = p[cc]
pd = p[d]
Delta = c(0, 0, 0, 0, 0, 0, 1,0, 0)
l2 = likJ(a,b,cc,d, pa,pb,pc,pd, Delta = Delta)
sum(l2) == 1

thoree/inbred documentation built on March 28, 2021, 7:42 p.m.