Nothing
poisson.CARlocalisedMCMC <- function(Y, offset, X.standardised, W, G, Gstar, K, N, N.all, p, burnin, n.sample, thin, MALA, prior.mean.beta, prior.var.beta, prior.delta, prior.tau2, verbose, chain)
{
#Rcpp::sourceCpp("src/CARBayesST.cpp")
#source("R/common.functions.R")
#library(spdep)
#library(truncnorm)
#
#
############################################
#### Set up the key elements before sampling
############################################
#### Compute the blocking structure for beta
if(!is.null(X.standardised))
{
## Compute the blocking structure for beta
block.temp <- common.betablock(p)
beta.beg <- block.temp[[1]]
beta.fin <- block.temp[[2]]
n.beta.block <- block.temp[[3]]
list.block <- as.list(rep(NA, n.beta.block*2))
for(r in 1:n.beta.block)
{
list.block[[r]] <- beta.beg[r]:beta.fin[r]-1
list.block[[r+n.beta.block]] <- length(list.block[[r]])
}
}else
{}
#### Compute a starting value for beta
if(!is.null(X.standardised))
{
mod.glm <- glm(Y~X.standardised-1, offset=offset, family="quasipoisson")
beta.mean <- mod.glm$coefficients
beta.sd <- sqrt(diag(summary(mod.glm)$cov.scaled))
beta <- rnorm(n=length(beta.mean), mean=beta.mean, sd=beta.sd)
regression.vec <- X.standardised %*% beta
}else
{
regression.vec <- rep(0, N.all)
}
#### Generate the initial parameter values
log.Y <- log(Y)
log.Y[Y==0] <- -0.1
res.temp <- log.Y - regression.vec - offset
clust <- kmeans(res.temp,G)
lambda <- clust$centers[order(clust$centers)]
lambda.mat <- matrix(rep(lambda, N), nrow=N, byrow=TRUE)
Z <- rep(1, N.all)
for(j in 2:G)
{
Z[clust$cluster==order(clust$centers)[j]] <- j
}
Z.mat <- matrix(Z, nrow=K, ncol=N, byrow=FALSE)
mu <- matrix(lambda[Z], nrow=K, ncol=N, byrow=FALSE)
res.sd <- sd(res.temp, na.rm=TRUE)/5
phi.mat <- matrix(rnorm(n=N.all, mean=0, sd = res.sd), nrow=K, byrow=FALSE)
phi <- as.numeric(phi.mat)
tau2 <- var(phi)/10
gamma <- runif(1)
delta <- runif(1,1, min(2, prior.delta))
#### Specify matrix quantities
Y.mat <- matrix(Y, nrow=K, ncol=N, byrow=FALSE)
offset.mat <- matrix(offset, nrow=K, ncol=N, byrow=FALSE)
regression.mat <- matrix(regression.vec, nrow=K, ncol=N, byrow=FALSE)
#### Matrices to store samples
n.keep <- floor((n.sample - burnin)/thin)
samples.Z <- array(NA, c(n.keep, N.all))
samples.lambda <- array(NA, c(n.keep, G))
samples.delta <- array(NA, c(n.keep, 1))
samples.tau2 <- array(NA, c(n.keep, 1))
samples.gamma <- array(NA, c(n.keep, 1))
samples.phi <- array(NA, c(n.keep, N.all))
samples.fitted <- array(NA, c(n.keep, N.all))
samples.loglike <- array(NA, c(n.keep, N.all))
#### Specify the Metropolis quantities
if(!is.null(X.standardised))
{
samples.beta <- array(NA, c(n.keep, p))
accept <- rep(0,8)
proposal.corr.beta <- solve(t(X.standardised) %*% X.standardised)
chol.proposal.corr.beta <- chol(proposal.corr.beta)
proposal.sd.beta <- 0.01
}else
{
accept <- rep(0,6)
}
proposal.sd.lambda <- 0.1
proposal.sd.delta <- 0.1
proposal.sd.phi <- 0.1
Y.extend <- matrix(rep(Y, G), byrow=F, ncol=G)
delta.update <- matrix(rep(1:G, N.all-K), ncol=G, byrow=T)
tau2.posterior.shape <- prior.tau2[1] + N * (K-1) /2
#### CAR quantities
W.quants <- common.Wcheckformat.leroux(W)
W <- W.quants$W
W.triplet <- W.quants$W.triplet
W.n.triplet <- W.quants$n.triplet
W.triplet.sum <- W.quants$W.triplet.sum
n.neighbours <- W.quants$n.neighbours
W.begfin <- W.quants$W.begfin
#### Start timer
if(verbose)
{
cat("\nMarkov chain", chain, "- generating", n.keep, "post burnin and thinned samples.\n", sep = " ")
progressBar <- txtProgressBar(style = 3)
percentage.points<-round((1:100/100)*n.sample)
}else
{
percentage.points<-round((1:100/100)*n.sample)
}
##############################
#### Generate the MCMC samples
##############################
#### Create the MCMC samples
for(j in 1:n.sample)
{
####################
## Sample from beta
####################
if(!is.null(X.standardised))
{
offset.temp <- offset + as.numeric(mu) + as.numeric(phi.mat)
if(MALA)
{
temp <- poissonbetaupdateMALA(X.standardised, N.all, p, beta, offset.temp, Y, prior.mean.beta, prior.var.beta, n.beta.block, proposal.sd.beta, list.block)
}else
{
temp <- poissonbetaupdateRW(X.standardised, N.all, p, beta, offset.temp, Y, prior.mean.beta, prior.var.beta, n.beta.block, proposal.sd.beta, list.block)
}
beta <- temp[[1]]
accept[7] <- accept[7] + temp[[2]]
accept[8] <- accept[8] + n.beta.block
regression.vec <- X.standardised %*% beta
regression.mat <- matrix(regression.vec, nrow=K, ncol=N, byrow=FALSE)
}else
{}
#######################
#### Sample from lambda
#######################
#### Propose a new value
proposal.extend <- c(-100, lambda, 100)
for(r in 1:G)
{
proposal.extend[(r+1)] <- rtruncnorm(n=1, a=proposal.extend[r], b=proposal.extend[(r+2)], mean=proposal.extend[(r+1)], sd=proposal.sd.lambda)
}
proposal <- proposal.extend[-c(1, (G+2))]
#### Compute the data likelihood
lp.current <- lambda[Z] + offset + as.numeric(regression.mat) + as.numeric(phi.mat)
lp.proposal <- proposal[Z] + offset + as.numeric(regression.mat) + as.numeric(phi.mat)
like.current <- Y * lp.current - exp(lp.current)
like.proposal <- Y * lp.proposal - exp(lp.proposal)
prob <- exp(sum(like.proposal - like.current))
if(prob > runif(1))
{
lambda <- proposal
lambda.mat <- matrix(rep(lambda, N), nrow=N, byrow=TRUE)
mu <- matrix(lambda[Z], nrow=K, ncol=N, byrow=FALSE)
accept[1] <- accept[1] + 1
}else
{}
accept[2] <- accept[2] + 1
##################
#### Sample from Z
##################
prior.offset <- rep(NA, G)
for(r in 1:G)
{
prior.offset[r] <- log(sum(exp(-delta * ((1:G - r)^2 + (1:G - Gstar)^2))))
}
mu.offset <- exp(offset.mat + regression.mat + phi.mat)
test <- Zupdatesqpoi(Z=Z.mat, Offset=mu.offset, Y=Y.mat, delta=delta, lambda=lambda, nsites=K, ntime=N, G=G, SS=1:G, prioroffset=prior.offset, Gstar=Gstar)
Z.mat <- test
Z <- as.numeric(Z.mat)
mu <- matrix(lambda[Z], nrow=K, ncol=N, byrow=FALSE)
######################
#### Sample from delta
######################
proposal.delta <- rtruncnorm(n=1, a=1, b=prior.delta, mean=delta, sd=proposal.sd.delta)
sum.delta1 <- sum((Z - Gstar)^2)
sum.delta2 <- sum((Z.mat[ ,-1] - Z.mat[ ,-N])^2)
current.fc1 <- -delta * (sum.delta1 + sum.delta2) - K * log(sum(exp(-delta * (1:G - Gstar)^2)))
proposal.fc1 <- -proposal.delta * (sum.delta1 + sum.delta2) - K * log(sum(exp(-proposal.delta * (1:G - Gstar)^2)))
Z.temp <- matrix(rep(as.numeric(Z.mat[ ,-N]),G), ncol=G, byrow=FALSE)
Z.temp2 <- (delta.update - Z.temp)^2 + (delta.update - Gstar)^2
current.fc <- current.fc1 - sum(log(apply(exp(-delta * Z.temp2),1,sum)))
proposal.fc <- proposal.fc1 - sum(log(apply(exp(-proposal.delta * Z.temp2),1,sum)))
hastings <- log(dtruncnorm(x=delta, a=1, b=prior.delta, mean=proposal.delta, sd=proposal.sd.delta)) - log(dtruncnorm(x=proposal.delta, a=1, b=prior.delta, mean=delta, sd=proposal.sd.delta))
prob <- exp(proposal.fc - current.fc + hastings)
if(prob > runif(1))
{
delta <- proposal.delta
accept[3] <- accept[3] + 1
}else
{}
accept[4] <- accept[4] + 1
####################
#### Sample from phi
####################
phi.offset <- mu + offset.mat + regression.mat
temp1 <- poissonar1carupdateRW(W.triplet, W.begfin, W.triplet.sum, K, N, phi.mat, tau2, gamma, 1, Y.mat, proposal.sd.phi, phi.offset, W.triplet.sum)
phi.temp <- temp1[[1]]
phi <- as.numeric(phi.temp)
for(i in 1:G)
{
phi[which(Z==i)] <- phi[which(Z==i)] - mean(phi[which(Z==i)])
}
phi.mat <- matrix(phi, nrow=K, ncol=N, byrow=FALSE)
accept[5] <- accept[5] + temp1[[2]]
accept[6] <- accept[6] + K*N
####################
## Sample from gamma
####################
temp2 <- gammaquadformcompute(W.triplet, W.triplet.sum, W.n.triplet, K, N, phi.mat, 1)
mean.gamma <- temp2[[1]] / temp2[[2]]
sd.gamma <- sqrt(tau2 / temp2[[2]])
gamma <- rtruncnorm(n=1, a=0, b=1, mean=mean.gamma, sd=sd.gamma)
####################
## Samples from tau2
####################
temp3 <- tauquadformcompute(W.triplet, W.triplet.sum, W.n.triplet, K, N, phi.mat, 1, gamma)
tau2.posterior.scale <- temp3 + prior.tau2[2]
tau2 <- 1 / rgamma(1, tau2.posterior.shape, scale=(1/tau2.posterior.scale))
#########################
## Calculate the deviance
#########################
lp <- as.numeric(mu + offset.mat + regression.mat + phi.mat)
fitted <- exp(lp)
loglike <- dpois(x=as.numeric(Y), lambda=fitted, log=TRUE)
###################
## Save the results
###################
if(j > burnin & (j-burnin)%%thin==0)
{
ele <- (j - burnin) / thin
samples.delta[ele, ] <- delta
samples.lambda[ele, ] <- lambda
samples.Z[ele, ] <- Z
samples.phi[ele, ] <- as.numeric(phi.mat)
samples.tau2[ele, ] <- tau2
samples.gamma[ele, ] <- gamma
samples.fitted[ele, ] <- fitted
samples.loglike[ele, ] <- loglike
if(!is.null(X.standardised)) samples.beta[ele, ] <- beta
}else
{}
########################################
## Self tune the acceptance probabilties
########################################
if(ceiling(j/100)==floor(j/100) & j < burnin)
{
if(!is.null(X.standardised))
{
if(p>2)
{
proposal.sd.beta <- common.accceptrates1(accept[7:8], proposal.sd.beta, 40, 50)
}else
{
proposal.sd.beta <- common.accceptrates1(accept[7:8], proposal.sd.beta, 30, 40)
}
proposal.sd.phi <- common.accceptrates1(accept[5:6], proposal.sd.phi, 40, 50)
proposal.sd.lambda <- common.accceptrates2(accept[1:2], proposal.sd.lambda, 20, 40, 10)
proposal.sd.delta <- common.accceptrates2(accept[3:4], proposal.sd.delta, 40, 50, prior.delta/6)
accept <- rep(0,8)
}else
{
proposal.sd.phi <- common.accceptrates1(accept[5:6], proposal.sd.phi, 40, 50)
proposal.sd.lambda <- common.accceptrates2(accept[1:2], proposal.sd.lambda, 20, 40, 10)
proposal.sd.delta <- common.accceptrates2(accept[3:4], proposal.sd.delta, 40, 50, prior.delta/6)
accept <- rep(0,6)
}
}else
{}
################################
## print progress to the console
################################
if(j %in% percentage.points & verbose)
{
setTxtProgressBar(progressBar, j/n.sample)
}
}
############################################
#### Return the results to the main function
############################################
#### Compile the results
if(is.null(X.standardised)) samples.beta <- NA
chain.results <- list(samples.beta=samples.beta, samples.phi=samples.phi, samples.Z=samples.Z, samples.lambda=samples.lambda, samples.tau2=samples.tau2, samples.delta=samples.delta, samples.gamma=samples.gamma, samples.loglike=samples.loglike, samples.fitted=samples.fitted,
accept=accept)
#### Return the results
return(chain.results)
}
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