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Type 'q()' to quit R. > # test all of the runjags dispatch methods with a toy example: > > library(runjags) > > runjags.options(inits.warning=FALSE, rng.warning=FALSE, blockignore.warning=FALSE, silent.jags=TRUE) > > # Require for as.mcmc.list and niter: > 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, dic, popt, pd + }" > > model_parallel <- "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))) > > > # Get the JAGS path - rjags adds the JAGS path to the PATH in Windows... > try(library(rjags)) Linked to JAGS 4.3.1 Loaded modules: basemod,bugs > jagspath <- findjags() > > # Only run the JAGS methods tests if we have found JAGS and have permission to run it: > if(jagspath!="JAGS not found" && testjags(jagspath)$JAGS.available){ + + testnum <- 1 + cat('Testing the simple method\n') + # Try the simple method and if it doesn't work give a warning but don't fail (likely to be permissions problems) + success <- try({ + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='simple',temp=FALSE) + }) + if(inherits(success, 'try-error')){ + cat("JAGS was found but the simple method failed; it is possible that there were permissions issues or similar. Details as follows:\n") + t <- testjags(silent=FALSE) + cat(failed.jags('output')[[1]]) + print(file.info(jagspath)) + print(file.info(getwd())[,1:3]) + cat("All test methods (except possibly rjags) were skipped\n") + }else{ + cat('Running method test number', testnum, '\n'); testnum <- testnum+1 + stopifnot(niter(as.mcmc.list(results))==1000) + + cat('Running method test number', testnum, '\n'); testnum <- testnum+1 + results <- run.jags(model_parallel, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='parallel') + stopifnot(niter(as.mcmc.list(results))==1000) + + cat('Running method test number', testnum, '\n'); testnum <- testnum+1 + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='interruptible') + stopifnot(niter(as.mcmc.list(results))==1000) + + # Same as in checkinputs but it's for rjags there: + cat('Running method 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 method 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 method 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') + + # Same as in checkinputs but it's for rjags there: + cat('Running method test number', testnum, '\n'); testnum <- testnum+1 + results2 <- extend.jags(results, sample=1000, add.monitor="true.y", summarise=FALSE, method='simple') + 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 method 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 method 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') + + # Snow gives problems here ... but it does work! + #results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='snow') + #stopifnot(niter(as.mcmc.list(results))==1000) + + cat('Running method test number', testnum, '\n'); testnum <- testnum+1 + info <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='background') + t <- 0 + repeat{ + # Change thin, chain and variables: + s <- try(results <- results.jags(info, read.monitor='m', return.samples=100, recover.chains=2, summarise=FALSE)) + if(!inherits(s, 'try-error')) break + if(t==30) stop("Timed out waiting for the bgparallel method") + Sys.sleep(1) + t <- t+1 + } + stopifnot(niter(as.mcmc.list(results))==100) + stopifnot(nvar(as.mcmc.list(results))==1) + stopifnot(nchain(as.mcmc.list(results))==1) + + + cat('Running method test number', testnum, '\n'); testnum <- testnum+1 + info <- run.jags(model_parallel, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='bgparallel') + t <- 0 + repeat{ + s <- try(results <- results.jags(info)) + if(!inherits(s, 'try-error')) break + if(t==30) stop("Timed out waiting for the bgparallel method") + Sys.sleep(1) + t <- t+1 + } + stopifnot(niter(as.mcmc.list(results))==1000) + + # Check combine.mcmc does what it says on the tin: + stopifnot(niter(combine.mcmc(results, return.samples=1000, collapse.chains=TRUE))==1000) + stopifnot(niter(combine.mcmc(results, return.samples=11, collapse.chains=TRUE))==11) + stopifnot(niter(combine.mcmc(results, return.samples=100, collapse.chains=FALSE))==100) + stopifnot(niter(combine.mcmc(results, thin=1, collapse.chains=TRUE))==2000) + stopifnot(niter(combine.mcmc(results, thin=10, collapse.chains=TRUE))==200) + stopifnot((niter(combine.mcmc(results, thin=15, collapse.chains=TRUE))*15)>=2000) + stopifnot(niter(combine.mcmc(results, thin=10, collapse.chains=FALSE))==100) + + # Check we can use the extend wrapper: + cat('Running method test number', testnum, '\n'); testnum <- testnum+1 + newres <- extend.jags(results, sample=0) + stopifnot(newres$burnin==results$burnin) + stopifnot(niter(as.mcmc.list(newres))==niter(as.mcmc.list(results))) + + # Check a single iteration works: + cat('Running method test number', testnum, '\n'); testnum <- testnum+1 + results <- run.jags(model, n.chains=2, sample=1, burnin=1000, inits=initfunction, method='interruptible', summarise=FALSE) + stopifnot(niter(as.mcmc.list(results))==1) + + # And that precision can be ignored: + cat('Running method test number', testnum, '\n'); testnum <- testnum+1 + results <- run.jags(model, monitor=c('m','c'), n.chains=2, sample=10, burnin=100, inits=initfunction, method='interruptible', summarise=FALSE, noread.monitor='precision') + stopifnot(nvar(as.mcmc.list(results))==2) + + # Check the version number is correct: + cat('Running method test number', testnum, '\n'); testnum <- testnum+1 + stopifnot(newres$runjags.version[1]==runjags:::runjagsprivate$runjagsversion) + + } + }else{ + cat("JAGS could not be called externally at the path: ", jagspath, "\n") + cat("All test methods except possibly rjags and rjagsparallel were skipped\n") + } You are using R Under development (unstable) (2024-03-09 r86082 ucrt) on a windows machine, with the RTerm GUI JAGS version 4.3.1 found successfully using the command 'C:/Program Files/JAGS/JAGS-4.3.1/x64/bin/jags-terminal.exe' The rjags package is installed Testing the simple method Running the simulation using the simple method... (output will be displayed once the simulation has termianted) Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 1 Running method test number 2 Calling 2 simulations using the parallel method... All chains have finished Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 3 Calling the simulation... Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 4 Calling the simulation... Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 5 Calling the simulation... Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 6 Calling the simulation... Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 7 Running the simulation using the simple method... (output will be displayed once the simulation has termianted) Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 8 Calling the simulation... Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 9 Calling the simulation... Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 10 Starting the simulation in the background... d:\RCompile\CRANincoming\R-devel\runjags.Rcheck\tests\runjagsfiles>"C:/Program Files/JAGS/JAGS-4.3.1/x64/bin/jags-terminal.exe" sim.1/script.cmd 1>sim.1/jagsoutput.txt 2>&1 d:\RCompile\CRANincoming\R-devel\runjags.Rcheck\tests\runjagsfiles>"D:/RCompile/CRANincoming/R-devel/lib/runjags/xgrid/beep.bat"  The JAGS process is now running in the background Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 11 Starting 2 simulations in the background... d:\RCompile\CRANincoming\R-devel\runjags.Rcheck\tests\runjagsfiles>"C:/Program Files/JAGS/JAGS-4.3.1/x64/bin/jags-terminal.exe" sim.2/script.cmd 1>sim.2/jagsoutput.txt 2>&1 d:\RCompile\CRANincoming\R-devel\runjags.Rcheck\tests\runjagsfiles>"D:/RCompile/CRANincoming/R-devel/lib/runjags/xgrid/beep.bat"  The JAGS processes are now running in the background Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 12 Running method test number 13 Calling the simulation... Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 14 Calling the simulation... Simulation complete. Reading coda files... Coda files loaded successfully Finished running the simulation Running method test number 15 > > testnum <- 1 > if(require("rjags")){ + cat('Running rjags method test number', testnum, '\n'); testnum <- testnum+1 + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='rjags') + stopifnot(niter(as.mcmc.list(results))==1000) + + cat('Running rjags method test number', testnum, '\n'); testnum <- testnum+1 + results <- run.jags(model, n.chains=2, sample=1, burnin=1000, inits=initfunction, method='rjags', summarise=FALSE) + stopifnot(niter(as.mcmc.list(results))==1) + + cat('Running rjags method test number', testnum, '\n'); testnum <- testnum+1 + runjags.options(silent.jags=TRUE, silent.runjags=TRUE, debug=FALSE) + output <- capture.output(results <- run.jags(model_parallel, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='rjparallel')) + stopifnot(length(output)==0) + stopifnot(niter(as.mcmc.list(results))==1000) + }else{ + cat("The rjags and rjagsparallel method checks were skipped as the rjags package is not installed\n") + } Running rjags method test number 1 module dic loaded Finished running the simulation Running rjags method test number 2 Finished running the simulation Running rjags method test number 3 > > cat("All methods checks passed\n") All methods checks passed > > > proc.time() user system elapsed 4.68 1.37 57.06