Nothing
indep_sig <- function(X,y,priors,BTE = c(3000,100000,1), verb = 1, eps = sqrt(.Machine$double.eps)){
gamdraw <- function(x){
rinvgamma(1,shape = x[1], scale = x[2])
}
nDigits <- function(x){
truncX <- floor(abs(x))
if(truncX != 0){
floor(log10(truncX)) + 1
} else {
1
}
}
# Number of tests
K <- ncol(y[[1]])
## Sample Locations
N <- nrow(y[[1]])
## Components
M <- length(y)
burn <- BTE[1]
iters <- BTE[2]
thin <- BTE[3]
no.betas <- ncol(X)
x.unit <- X
X.unit <- as.matrix(bdiag(replicate(M,x.unit,simplify = FALSE)))
X <- do.call("rbind", replicate(K, X.unit, simplify=FALSE))
X.M <- list()
Sig <- list()
for(i in 1:M){
X.M[[i]] <- X.unit[((i-1)*N+1):(i*N),]
Sig[[i]] <- matrix(NA, nrow = N, ncol = iters)
}
ybar <- lapply(y,rowMeans)
Y <- do.call(cbind,y)
Y <- as.vector(Y)
beta <- replicate(M, matrix(NA, nrow = no.betas, ncol = iters), simplify = FALSE)
names(beta) <- names(Sig) <- names(y)
bhat <- as.vector(solve(t(X) %*% X) %*% t(X) %*% Y)
phi.priors <- list()
bhat[which(bhat < 0)] <- 0
if(priors == "Jeffreys"){
mu0 <- rep(0, length(bhat))
dgts <- sapply(bhat,nDigits)
V0i <- diag(length(dgts))*0
a0 <- 0
b0 <- 0
for(i in 1:M){
phi.priors[[i]] <- cbind.data.frame(a = rep(a0, times = N), b = rep(b0, times = N))
}
if(verb != 0){message("Jeffreys Priors Used\n")}
}else if(is.list(priors)){
phi.priors <- priors$phi
mu0 <- priors$beta$mu0
V0i <- solve(priors$beta$V0)
if(verb != 0){message("User Specified Priors Used\n")}
}else{
b0 <- 0.000001
a0 <- 0.000001
mu0 <- bhat
dgts <- sapply(bhat,nDigits)
V0i <- diag(1/(10^(dgts+6)))
for(i in 1:M){
phi.priors[[i]] <- cbind.data.frame(a = rep(a0, times = N), b = rep(b0, times = N))
}
if(verb != 0){message("Default Priors Used\n")}
}
bhat[which(bhat == 0)] <- eps
b.use <- bhat
V0imu0 <- V0i %*% mu0
alpha <- lapply(phi.priors, function(X){X[,1] + K/2})
rate <- rep(NA,N)
beta.temp <- rep(NA, times = no.betas*M)
if(verb != 0){
message("Sampling from posterior distributions")
pb <- txtProgressBar(min = 0, max = iters/100, initial = 0, style = 3)
step <- 0
}
for(t in 2:iters){
if(verb != 0 & (t/100) %% 1 == 0){
step <- step + 1
setTxtProgressBar(pb,value = step)
}
for(i in 1:M){
xB <- as.vector(X.M[[i]] %*% b.use)
for(j in 1:N){
rate[j] <- 0.5*(t(xB[j] - y[[i]][j,]) %*% (xB[j] - y[[i]][j,]) )+ phi.priors[[i]][j,2]
}
Sig[[i]][,t] <- s.temp <- apply(cbind(alpha[[i]],rate),1, gamdraw)
Wi <- diag(1/s.temp)
xtWix <- t(x.unit) %*% Wi %*% x.unit * K
precis <- xtWix + diag(diag(V0i)[((i - 1)*no.betas +1):(i*no.betas)])
cov.use <- solve(precis)
bhat <- cov.use %*% (V0imu0[((i - 1)*no.betas +1):(i*no.betas)] + t(x.unit)%*%Wi %*% ybar[[i]] * K)
beta.temp[((i - 1)*no.betas +1):(i*no.betas)] <- beta[[i]][,t] <- as.vector(
rtmvnorm(n = 1, mean = bhat[,1], sigma = cov.use, lower = rep(0, length = no.betas)))
}
b.use <- beta.temp
}
if(verb != 0){close(pb)}
Sig <- lapply(Sig,function(X, b){X[,-(1:b)]}, b = burn)
Sig <- lapply(Sig, function(X,t){X[,seq(from = 1, to = ncol(X), by = t)]}, t = thin)
beta <- lapply(beta,function(X, b){X[,-(1:b)]}, b = burn)
beta <- lapply(beta, function(X,t){X[,seq(from = 1, to = ncol(X), by = t)]}, t = thin)
samps <- list(beta = beta,
Sig = Sig,
priors= list(beta = list(mu0 = mu0, V0 = diag((1/diag(V0i)))), phi = phi.priors), cov.structure = "indep")
return(samps)
}
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