R Under development (unstable) (2024-03-09 r86082 ucrt) -- "Unsuffered Consequences"
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> # First load runjags and verify that the options can be set:
> library('runjags')
> runjags.options(inits.warning=FALSE, rng.warning=FALSE, silent.jags=TRUE)
> newopts <- runjags.options()
> stopifnot(newopts$inits.warning==FALSE)
> stopifnot(newopts$rng.warning==FALSE)
> stopifnot(newopts$silent.jags==TRUE)
> 
> 
> # Test some runjags inputs with the rjags method:
> 
> testnum <- 1
> if(require("rjags")){
+ 
+ 	# Required for nvar etc:
+ 	library("coda")
+ 
+ 	model <- "model {
+ 	for(i in 1 : N){ #data# N
+ 	Y[i] ~ dnorm(true.y[i], precision); #data# Y
+ 	true.y[i] <- (m * X[i]) + c; #data# X
+ 	}
+ 	m ~ dunif(-1000,1000); #inits# m
+ 	c ~ dunif(-1000,1000);
+ 	precision ~ dexp(1);
+ 	#monitor# m, c, precision
+ 	}"
+ 
+ 	# Simulate the data
+ 	X <- 1:100
+ 	Y <- rnorm(length(X), 2*X + 10, 1)
+ 	N <- length(X)
+ 
+ 	initfunction <- function(chain) return(switch(chain, "1"=list(m=-10), "2"=list(m=10)))
+ 	initfunction2 <- function() return(switch(sample(c(1,2),1), "1"=list(m=-10), "2"=list(m=10)))
+ 
+ 	datalist <- list(X=X, Y=Y, N=N)
+ 	
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='rjags')
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction2, method='rjags')
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=lapply(1:2,initfunction), method='rjags')
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction(1), method='rjags')
+ 
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction, method='rjags')
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction2, method='rjags')
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=lapply(1:2,initfunction), method='rjags')
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction(1), method='rjags')
+ 	stopifnot(nvar(as.mcmc.list(results))==(3))
+ 	stopifnot(all(varnames(as.mcmc.list(results))==c('m','c','precision')))
+ 
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results <- extend.jags(results,sample=1000)
+ 	stopifnot(niter(as.mcmc.list(results))==2000)
+ 	stopifnot(nvar(as.mcmc.list(results))==3)
+ 
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results2 <- extend.jags(results, sample=1000, drop.chain=1, summarise=FALSE)
+ 	stopifnot(nchain(as.mcmc.list(results2))==1)
+ 	stopifnot(identical(list.format(results$end.state[[2]])$.RNG.name, list.format(results2$end.state[[1]])$.RNG.name))
+   
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results2 <- extend.jags(results, sample=1000, drop.monitor="precision", summarise=FALSE)
+ 	stopifnot(nvar(as.mcmc.list(results2))==2)
+   
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results2 <- extend.jags(results, sample=1000, add.monitor="true.y", summarise=FALSE)
+ 	stopifnot(nvar(as.mcmc.list(results2))==(3+N))
+ 	stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[103]=='true.y[100]')
+ 
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results2 <- extend.jags(results, sample=1000, add.monitor=c("true.y", "dic"), summarise=FALSE)
+ 	stopifnot(nvar(as.mcmc.list(results2))==(3+N))
+ 	stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[103]=='true.y[100]')
+ 
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results2 <- extend.jags(results, sample=1000, add.monitor=c("true.y", "deviance"), summarise=FALSE)
+ 	stopifnot(nvar(as.mcmc.list(results2))==(4+N))
+ 	stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[104]=='deviance')
+ 	
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction, method='rjparallel')
+ 	stopifnot(nvar(as.mcmc.list(results))==(3))
+ 	stopifnot(all(varnames(as.mcmc.list(results))==c('m','c','precision')))	
+ 
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results2 <- extend.jags(results, sample=1000, add.monitor="true.y", summarise=FALSE, method='rjp')
+ 	stopifnot(nvar(as.mcmc.list(results2))==(3+N))
+ 	stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[103]=='true.y[100]')
+ 	
+ 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
+ 	results2 <- extend.jags(results, sample=1000, add.monitor=c("true.y", "deviance"), summarise=FALSE, method='rjp')
+ 	stopifnot(nvar(as.mcmc.list(results2))==(4+N))
+ 	stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[104]=='deviance')
+ 	
+ 	cat("All input checks passed\n")
+ 
+ }else{
+ 	cat("The input checks were not performed as rjags is not installed\n")
+ }
Loading required package: rjags
Loading required package: coda
Linked to JAGS 4.3.1
Loaded modules: basemod,bugs
Running input test number 1 
Finished running the simulation
Running input test number 2 
Finished running the simulation
Running input test number 3 
Finished running the simulation
Running input test number 4 
Finished running the simulation
Running input test number 5 
Finished running the simulation
Running input test number 6 
Finished running the simulation
Running input test number 7 
Finished running the simulation
Running input test number 8 
Finished running the simulation
Running input test number 9 
Finished running the simulation
Running input test number 10 
Finished running the simulation
Running input test number 11 
Finished running the simulation
Running input test number 12 
Finished running the simulation
Running input test number 13 
module dic loaded
Finished running the simulation
Running input test number 14 
Finished running the simulation
Running input test number 15 
Starting 2 rjags simulations using a PSOCK cluster with 2 nodes on host
'localhost'
Finished running the simulation
Running input test number 16 
Starting 2 rjags simulations using a PSOCK cluster with 2 nodes on host
'localhost'
Finished running the simulation
Running input test number 17 
Starting 2 rjags simulations using a PSOCK cluster with 2 nodes on host
'localhost'
Finished running the simulation
All input checks passed
> 
> proc.time()
   user  system elapsed 
  10.96    0.64   31.42