Carry out the forward-backward algorithm for the HMM implied by knowing the two parental haplotypes.
forward_backward_(x, p1, p2, d, p, lambda, epsilon, start, end)
| x | 0-1 vector of length p giving the offspring haplotypes |
|---|---|
| p1 | 0-1 vector of length p giving one parental haplotype |
| p2 | 0-1 vector of length p giving the other parental haplotype |
| d | numberic vector of length p - 1 giving the distance between each site |
| p | length of the vector x |
| lambda | the recombination rate, a multiplier for the distance d |
| epsilon | the pointwise mutation rate |
| start | indexes of the subset of x to perform the computation (1 indexed) |
| end | indexes of the subset of x to perform the computation (1 indexed) |
p1_start: the probability that the latent state immediately before the specified window is 1, i.e. the offspring is being copied from p1.
p1_start_odd: probability of an odd number of recombinations given that the latent state immediately before the specified window is 1.
p2_start_odd: probability of an odd number of recombinations given that the latent state immediately before the specified window is 2.