Nothing
hmm.vitFUN.rils <-
function (geno, position, geno.probability, transitionFUN = phy2get.haldane.rils,
emissionFUN = makeEmissionFUN(errorRate = 0.01), ...)
{
n.obs <- length(geno)
n.state <- length(geno.probability)
psi <- delta <- matrix(0, nrow = n.state, ncol = n.obs)
n.con <- geno.cr <- numeric(n.obs)
geno.dis <- abs(diff(position))
n.con[1] <- 1
g <- geno[1]
for (i in 2:n.obs) {
n.con[i] <- ifelse(geno[i] == g, n.con[i - 1] + 1, 1)
g <- geno[i]
}
for (i in 1:n.state) delta[i, 1] <- log(geno.probability[i]) +
emissionFUN(i, geno[1], n.con[1])
preProb <- numeric(n.state)
for (t in 2:n.obs) {
for (j in 1:n.state) {
for (i in 1:n.state) preProb[i] <- delta[i, t - 1] +
log(transitionFUN(i, j, geno.dis[t - 1]))
psi[j, t] <- which.max(preProb)
delta[j, t] <- max(preProb) + emissionFUN(j, geno[t],
n.con[t])
}
}
geno.cr[n.obs] <- which.max(delta[, n.obs])
for (t in seq(n.obs - 1, 1, by = -1)) geno.cr[t] <- psi[geno.cr[t +
1], t + 1]
geno.cr
}
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