implements a simple heterozygote miscall model with a modification for Mendelian incompatibilities

Note that the pure heterozygote miscall model is a little bit silly because alternate homozygotes have no chance of carrying another allele which leads to some issues with in the context of parentage inference because for non-parentals, it can lead to probability of zero for Mendelian incompatibilities. So, we start off with a pure heterozygote miscall model, and then we replace zeroes in each row with smidge divided by the number of zeroes. We basically just don't want to have any zeros because that could lead to probabilities of zero.

ge_model_pure_het_miscall(L, m, smidge)

Arguments

L

required locus specific information

m

the heterozygote miscall rate

smidge

the total amount added to zeroes in a row.

Examples

L <- list(
 freqs = c(A = 0.6, B = 0.4),
 geno_freqs = c(`A / A` = 0.36, `A / B` = 0.48, `B / B` = 0.16)
)
ge_model_pure_het_miscall(L, m = 0.0285, smidge = 0.001)
#>              A / A        A / B        B / B
#> A / A 0.9990009990 0.0004995005 0.0004995005
#> A / B 0.0142500000 0.9715000000 0.0142500000
#> B / B 0.0004995005 0.0004995005 0.9990009990