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set.seed(123)
data(longley)
data <- list(gnp=longley$GNP, employed=longley$Employed, n=nrow(longley))
modfile <- tempfile()
writeLines("
model{
for (i in 1:n){
employed[i] ~ dnorm(mu[i], tau)
mu[i] <- alpha + beta*gnp[i]
}
alpha ~ dnorm(0, 0.00001)
beta ~ dnorm(0, 0.00001)
sigma ~ dunif(0,1000)
tau <- pow(sigma,-2)
}", con=modfile)
inits <- function(){
list(alpha=rnorm(1,0,1),beta=rnorm(1,0,1),sigma=runif(1,0,3))
}
params <- c('alpha','beta','sigma', 'mu')
nul <- capture.output(
out <- autojags(data = data, inits = inits, parameters.to.save = params,
model.file = modfile, n.chains = 3, n.adapt = 100, n.burnin=50,
iter.increment=10, n.thin = 2, verbose=FALSE))
ref <- readRDS("autojags_ref.Rds")
# Remove time/date based elements
out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
expect_identical(out[-c(17,18,21)], ref[-c(17,18,21)])
# codaOnly---------------------------------------------------------------------
nul<- capture.output(
out <- autojags(data = data, inits = inits, parameters.to.save = params,
model.file = modfile, n.chains = 3, n.adapt = 100, n.burnin=50,
iter.increment=10, n.thin = 2, verbose=FALSE, codaOnly=c("mu")))
ref <- readRDS("autojags_ref_codaonly.Rds")
# Remove time/date based elements
out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
expect_identical(out[-c(17,18,21)], ref[-c(17,18,21)])
# Check recovery after process_output errors-----------------------------------
# Setting DIC to -999 forces process_output to error for testing
expect_message(nul<- capture.output(
out <- autojags(data = data, inits = inits, parameters.to.save = params,
model.file = modfile, n.chains = 3, n.adapt = 100, n.burnin=50,
iter.increment=10, n.thin = 2, verbose=FALSE, codaOnly=c("mu"), DIC=-999)))
expect_inherits(out, "jagsUIbasic")
expect_equal(coda::varnames(out$samples),
c("alpha","beta", "sigma", paste0("mu[",1:16,"]"),"deviance"))
expect_equal(names(out), c("samples", "model"))
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