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# Estimate compare Li and Horvitz 1953
# Compare calculation in Wang 2002 equation (15). It is based on Li et al 1993 and Lynch 1988 and is denoted as LL in Coancestry
Bxy <- function(row, data, pop1, pop2, allele.column, ref.pop=NA)
{
a <- allele.column*2+1
re <- .subset2(data,1)[row]
rat <- .subset2(data,2)[row]
ai <- .subset2(pop1,a)[re]
aj <- .subset2(pop1,a+1)[re]
bi <- .subset2(pop2,a)[rat]
bj <- .subset2(pop2,a+1)[rat]
# Estimate compare Li and Horvitz 1953
# Similarity is given by:
# 1,1 - 1,2 : 0.5
# 1,2 - 1,2 : 0.5
# 1,2 - 1,3 : 0.25
# 1,1 - 1,1 : 1
# Rest : 0
((ai==bi)+(ai==bj)+(aj==bi)+(aj==bj))/4
}
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