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posteriorchineseAFT.R
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posteriorchineseAFT = function(c,Y,mu,S,alpha,That, beta0, betahat, sigma2, lambda2, tau2, K, epsilon, W, beta, ro,D, r, si, Time,N, sig2.dat) {
Ytemp <- matrix(NA, nrow = N, ncol = D)
ctemp <- c
## This can't be parallelized !!!!!
for(l in 1:N) {
temp <- ctemp[l]
cminus <- ctemp
cminus[l] <- NA
## The table function helps converting the data point specific indicator variables to class specific indicator variables
g <- table(factor(cminus, levels = 1:K))
active <- which(g!=0)
kminus <- length(active)
## Two Auxilary Variables
## The name of the auxilary variables are taken to be one and two more than the maximum value in the already active cluster set
active <- append(active, max(active)+1)
active <- append(active, max(active)+1)
## If the observation was singelton (i.e no other point was associated with it then we assign to kminus +1 parameter)
if(length(which(cminus==temp))==0 || length(which(cminus==temp))==1 )
{
## The kminus+1 parameter gets the value of the temporary variable
ctemp[l] <- active[kminus+1]
mu[active[kminus+1],1:D] <- mu[temp,1:D]
S[active[kminus]+1,1:D,1:D] <- S[temp,1:D,1:D]
beta0[active[kminus+1]] <- beta0[temp]
betahat[active[kminus+1], 1:D] <- betahat[temp, 1:D]
sigma2[active[kminus+1]] <- sigma2[temp]
lambda2[active[kminus+1]] <- lambda2[temp]
tau2[active[kminus+1], 1:D] <- tau2[temp, 1:D]
## Also the second auxilary variable should be drawn from the prior distribution
source('priordraw.R')
priorone <- NA
priorone <- priordraw(beta, W, epsilon, ro, r, si,N,D, sig2.dat)
mu[active[kminus+2],1:D] <- priorone$mu
S[active[kminus+2],1:D,1:D] <- priorone$Sigma
beta0[active[kminus+2]] <- priorone$beta0
sigma2[active[kminus+2]] <- priorone$sigma2
betahat[active[kminus+2],1:D] <- priorone$betahat
lambda2[active[kminus+2]] <- priorone$lambda2
tau2[active[kminus+2], 1:D] <- priorone$tau2
## As we have to deal with centred matrices and if this point is alone in its cluster then
for ( k in 1:D){
Ytemp[l,k] <- 0
}
}else{
## We have to deal with centred matrices
clust <- which(ctemp == temp)
tempmatrix <- Y[clust,1:D]
sd.tempmatrix <- apply(tempmatrix, 2, function(x) sd(x))
mean.tempmatrix <- apply(tempmatrix, 2, mean)
for ( k in 1:D){
if (sd.tempmatrix[k] == 0){
sd.tempmatrix[k] = 1
}
}
for ( k in 1:D){
Ytemp[l,k] <- (Y[l,k] - mean.tempmatrix[k])/(sd.tempmatrix[k])
}
source('priordraw.R')
priortwo <- NA
priortwo <- priordraw(beta, W, epsilon, ro, r, si,N,D, sig2.dat)
mu[active[kminus+1],1:D] <- priortwo$mu
S[active[kminus+1],1:D,1:D] <- priortwo$Sigma[1:D,1:D]
beta0[active[kminus+1]] <- priortwo$beta0
sigma2[active[kminus+1]] <- priortwo$sigma2
betahat[active[kminus+1],1:D] <- priortwo$betahat
lambda2[active[kminus+1]] <- priortwo$lambda2
tau2[active[kminus+1], 1:D] <- priortwo$tau2
source('priordraw.R')
priorthree <- NA
priorthree <- priordraw(beta, W, epsilon, ro, r, si,N,D, sig2.dat)
mu[active[kminus+2],1:D] <- priorthree$mu
S[active[kminus+2],1:D,1:D] <- priorthree$Sigma[1:D,1:D]
beta0[active[kminus+2]] <- priorthree$beta0
sigma2[active[kminus+2]] <- priorthree$sigma2
betahat[active[kminus+2],1:D] <- priorthree$betahat
lambda2[active[kminus+2]] <- priorthree$lambda2
tau2[active[kminus+2], 1:D] <- priorthree$tau2
}
#######################################################
posterior <- matrix(NA, nrow = length(active), ncol = 1)
## Calculating the probabalities for drawing the value of c_i from the active classes
for (j in 1:kminus) {
res <- try(dMVN(as.vector(t(Y[l,1:D])), mean = mu[active[j],1:D], Q = S[active[j],1:D,1:D]), silent=TRUE)
if (class(res) == "try-error"){
posterior[j] <- 0
} else{
posterior[j] <- g[active[j]] /(N-1+alpha) * dMVN(as.vector(t(Y[l,1:D])), mean = mu[active[j],1:D], Q = S[active[j],1:D,1:D]) * dnorm(x = That[l], mean = beta0[active[j]] + betahat[active[j],1:D] %*% as.vector(t(Ytemp[l,1:D])), sd = sqrt(sigma2[active[j]]) )
}
}
res <- try(dMVN(as.vector(t(Y[l,1:D])), mean = mu[active[kminus+1],1:D], Q= S[active[kminus+1],1:D,1:D]), silent=TRUE)
if (class(res) == "try-error"){
posterior[kminus+1] <- 0
} else{
posterior[kminus+1] <- (0.5 * alpha) /(N-1+alpha) * dMVN(as.vector(t(Y[l,1:D])), mean = mu[active[kminus+1],1:D], Q= S[active[kminus+1],1:D,1:D]) * dnorm(x = That[l], mean = beta0[active[kminus+1]] + betahat[active[kminus+1],1:D] %*% as.vector(t(Ytemp[l,1:D])), sd = sqrt(sigma2[active[kminus+1]]) )
}
res2 <- try(dMVN(as.vector(t(Y[l,1:D])), mean = mu[active[kminus+2],1:D], Q= S[active[kminus+2],1:D,1:D]), silent=TRUE)
if (class(res2) == "try-error"){
posterior[kminus+2] <- 0
} else{
posterior[kminus+2] <- (0.5 * alpha) /(N-1+alpha) * dMVN(as.vector(t(Y[l,1:D])), mean = mu[active[kminus+2],1:D], Q = S[active[kminus+2],1:D,1:D]) * dnorm(x = That[l], mean = beta0[active[kminus+2]] + betahat[active[kminus+2],1:D] %*% as.vector(t(Ytemp[l,1:D])), sd = sqrt(sigma2[active[kminus+2]]) )
}
# posterior[kminus+1] <- (0.5 * alpha) /(N-1+alpha) * dMVN(as.vector(t(Y[l,1:D])), mean = mu[active[kminus+1],1:D], Q= S[active[kminus+1],1:D,1:D]) * dnorm(x = That[l], mean = beta0[active[kminus+1]] + betahat[active[kminus+1],1:D] %*% as.vector(t(Ytemp[l,1:D])), sd = sqrt(sigma2[active[kminus+1]]) )
#
# posterior[kminus+2] <- (0.5 * alpha) /(N-1+alpha) * dMVN(as.vector(t(Y[l,1:D])), mean = mu[active[kminus+2],1:D], Q = S[active[kminus+2],1:D,1:D]) * dnorm(x = That[l], mean = beta0[active[kminus+2]] + betahat[active[kminus+2],1:D] %*% as.vector(t(Ytemp[l,1:D])), sd = sqrt(sigma2[active[kminus+2]]) )
#
## Calculating the normalization constant for probabilities
normalization <- sum(posterior)
if (normalization < 1e-200 || normalization ==Inf){
ctemp[l] <- sample(active, 1, prob = rep(1,length(active)), replace = TRUE)
} else {
ctemp[l] <- sample(active, 1, prob= posterior, replace = TRUE)
}
}
c <- ctemp
## Delete those observations that are not associcated with no data point
g <- table(factor(c, levels = 1:K))
inactive <- which(g==0)
for ( i in 1:length(inactive)){
mu[inactive[i],1:D] <- NA
S[inactive[i],1:D,1:D] <- NA
beta0[inactive[i]] <- NA
sigma2[inactive[i]] <- NA
betahat[inactive[i],1:D] <- NA
lambda2[inactive[i]] <- NA
tau2[inactive[i], 1:D] <- NA
}
list('indicator' = c,'mean' = mu,'precision' = S, 'beta0' = beta0,'betahat2'= betahat, 'sigma2'=sigma2, 'lambda2'= lambda2, 'tau2' = tau2)
}