Nothing
inte <- function(yunique, n.yunique, ymatch, mu, sigma, n){
n.yunique <- length(yunique)
alpha <- seq(0, 1, length=n+1)
sigma2 <- sigma^2
mu <- alpha * mu[1] + (1 - alpha) * mu[2]
sigma <- sqrt(alpha^2 * sigma2[1] + (1 - alpha)^2 * sigma2[2])
dn <- getDen(yunique, n.yunique, 1:n.yunique, mu, sigma)
den <- apply(dn, 1, function(x) (sum(2 * x) - x[1] - x[n+1]) / (2 * n) )
den <- den[ymatch]
den
}
mritc.pvhmrfem <- function(y, neighbors, blocks,
spatialMat=matrix(c(2, 1, -1, -1, -1, 1, 2, 1, -1, -1,
-1, 1, 2, 1, -1, -1, -1, 1, 2, 1, -1, -1, -1, 1, 2),
ncol=5), beta=0.6,
mu, sigma, err=1e-4, maxit=20, verbose){
#Error checking
if (length(err) < 2) err <- rep(err, length.out = 2)
k <- length(mu) + 2
nneigh <- ncol(neighbors)
nblocks <- length(blocks)
neighbors <- structure(as.integer(neighbors), dim = dim(neighbors))
yunique <- sort(unique(y))
n.yunique <- length(yunique)
nvert <- length(y)
ymatch <- match(y, yunique)
muold <- rep(0,k-2)
sigmaold <- rep(0,k-2)
niter <- 10
check <- getCheck(nneigh, k, beta, spatialMat)
indices <- initialIndices(y, nvert, mu, sigma, k, sub=FALSE, type="partial")
it <- 0
repeat{
it <- it + 1
muold <- mu
sigmaold <- sigma
den.part <- getDen(yunique, n.yunique, ymatch, mu, sigma)
den <- matrix(0, nrow=nvert, ncol=k)
den[,1] <- den.part[,1]
den[,3] <- den.part[,2]
den[,5] <- den.part[,3]
den[,2] <- inte(yunique, n.yunique, ymatch, mu[1:2], sigma[1:2], 100)
den[,4] <- inte(yunique, n.yunique, ymatch, mu[2:3], sigma[2:3], 100)
for(j in 1:niter){
indices <- updateIndicesHMRFEM(neighbors, nneigh, blocks, nblocks, as.integer(k), indices, check, den)
}
prob <- updateProbs(neighbors, nneigh, indices, den, k, check)
mu <- updateMus(prob[,c(1,3,5)], y)
sigma <- updateSds(prob[,c(1,3,5)], y, mu, nvert, k-2)
flag <- checkStopVerbose(muold, mu, sigmaold, sigma, err, it, maxit, verbose)
if(flag==1) break
}
list(prob=prob, mu=mu, sigma=sigma)
}
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