Nothing
chib_indep <- function(s.l,X,y, verb){
beta <- do.call(rbind,s.l$beta)
Sig <- s.l$Sig
x.unit <- X
Bprior <- s.l$priors$beta
Sprior <- s.l$priors$phi
### Components
M <- length(Sig)
### Locations
N <- nrow(y[[1]])
### Number of tests
K <- ncol(y[[1]])
T <- ncol(beta)
P <- nrow(beta)
p.M <- P/M
### Define Ybar and X
Y <- do.call(rbind,y)
Ybar <- apply(Y,1,mean)
Y <- as.vector(Y)
yibar <- lapply(y,rowMeans)
X.unit <- bdiag(replicate(M,x.unit,simplify = FALSE))
X <- do.call("rbind", replicate(K, X.unit, simplify=FALSE))
## Prior Hyperparameters
S0 <- Bprior$V0
B0 <- Bprior$mu0
S0i <- solve(S0)
S0iB0 <- S0i %*% B0
### Initialize
p.int <- rep(NA, times = M)
B.bar <- apply(beta,1,mean)
Sig.bar <- list()
for(j in 1:M){
Sig.bar[[j]] <- apply(Sig[[j]],1,mean)
}
Sig.barfull <- list()
Si.full <- Bcov.full <- list()
S <- matrix(NA, N,N)
postB <- rep(NA, times = T)
lpost.Sig <- rep(NA, times = M)
lprior.Sig <- rep(NA, times = M)
rate <- rep(NA, times = N)
if(verb != 0){
message("Approximating integral for log-marignal likelihood")
pb <- txtProgressBar(min = 0, max = T/100, initial = 0, style = 3)
step <- 0
}
for(t in 1:T){
if(verb != 0 & (t/100) %% 1 == 0){
step <- step + 1
setTxtProgressBar(pb,value = step)
}
for(i in 1:M){
Si <- diag(1/Sig[[i]][,t])
xtSix <- t(x.unit) %*% Si %*% x.unit * K
#xtSixi <- solve(xtSix)
S0i.use <- diag(S0i)[((i-1)*p.M+1):(i*p.M)]
S0iB0.use <- S0iB0[((i-1)*p.M+1):(i*p.M)]
cov.use <- solve(xtSix + diag(S0i.use))
bhat <- cov.use %*% (S0iB0.use + t(x.unit)%*%Si %*% yibar[[i]] * K)
p.int[i] <- dtmvnorm(B.bar[((i-1)*p.M + 1):(i*p.M)], mean = bhat[,1], sigma = cov.use, lower = rep(0, times= p.M), log = TRUE)
}
postB[t] <- sum(p.int)
}
if(verb != 0){close(pb)}
lpostB <- log(mean(exp(postB)))
for(i in 1:M){
s <- Sig.bar[[i]]
B.use <- B.bar[(((i-1)*p.M)+1):(i*p.M)]
xB <- x.unit %*% B.use
for(j in 1:N){
rate[j] <- 0.5*(t(xB[j] - y[[i]][j,]) %*% (xB[j] - y[[i]][j,]) )+ Sprior[[i]]$b[j]
}
shape <- N/2 + Sprior[[i]]$a
lpost.Sig[i] <- sum(dinvgamma(s,shape = shape, scale = rate, log = TRUE))
lprior.Sig[i] <- sum(dinvgamma(s,shape = Sprior[[i]]$a,scale = Sprior[[i]]$b, log = TRUE))
}
lpriorB <- dtmvnorm(B.bar, mean = B0, sigma = S0, lower =rep(0, times = P), log = TRUE)
lpost <- sum(lpost.Sig) + lpostB
lprior <- sum(lprior.Sig) + lpriorB
Omega <- do.call("c",Sig.bar)
Omega <- rep(Omega, times = K)
Omega <- diag(Omega)
llik <- dtmvnorm(Y,mean = as.numeric(X%*%B.bar), sigma = Omega, lower =rep(0, times = length(Y)), log = TRUE)
lml <- llik + lprior - lpost
return(list(lpost = lpost, llik = llik, lprior =lprior, lml= lml))
}
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