diff options
Diffstat (limited to 'inst/tinytest/test_jags.R')
| -rw-r--r-- | inst/tinytest/test_jags.R | 45 |
1 files changed, 30 insertions, 15 deletions
diff --git a/inst/tinytest/test_jags.R b/inst/tinytest/test_jags.R index 6d57a6a..fab9e35 100644 --- a/inst/tinytest/test_jags.R +++ b/inst/tinytest/test_jags.R @@ -1,3 +1,4 @@ +at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" ) set.seed(123) data(longley) @@ -32,7 +33,10 @@ ref <- readRDS("longley_reference_fit.Rds") # Remove time/date based elements out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins -expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)]) + +if(at_home){ + expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)]) +} # Plots pdf(NULL) @@ -69,13 +73,15 @@ expect_equal(out$summary[,"sd"], coda_sum$statistics[,"SD"]) expect_equal(out$summary[,"50%"], coda_sum$quantiles[,"50%"]) # codaOnly--------------------------------------------------------------------- -out <- jags(data = data, inits = inits, parameters.to.save = params, +if(at_home){ + out <- jags(data = data, inits = inits, parameters.to.save = params, model.file = modfile, n.chains = 3, n.adapt = 100, n.iter = 100, n.burnin = 50, n.thin = 1, codaOnly=c("mu", "sigma"), verbose=FALSE) -ref <- readRDS("reference_codaOnly.Rds") + ref <- readRDS("reference_codaOnly.Rds") -out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins -expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)]) + out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins + expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)]) +} # DIC = FALSE------------------------------------------------------------------ out <- jags(data = data, inits = inits, parameters.to.save = params, @@ -83,32 +89,41 @@ out <- jags(data = data, inits = inits, parameters.to.save = params, n.burnin = 50, n.thin = 1, DIC=FALSE, verbose=FALSE) expect_false(out$calc.DIC) -ref <- readRDS("reference_noDIC.Rds") -out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins -expect_equal(out[-c(15,16,19)], ref[-c(15,16,19)]) +if(at_home){ + ref <- readRDS("reference_noDIC.Rds") + out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins + expect_equal(out[-c(15,16,19)], ref[-c(15,16,19)]) +} # Reordered parameter names---------------------------------------------------- pars_new <- c("mu", "sigma", "alpha", "beta") out <- jags(data = data, inits = inits, parameters.to.save = pars_new, model.file = modfile, n.chains = 3, n.adapt = 100, n.iter = 100, n.burnin = 50, n.thin = 1, verbose=FALSE) -ref <- readRDS("reference_parsorder.Rds") +expect_equal(c(paste0("mu[",1:16,"]"), "sigma","alpha","beta","deviance"), + colnames(out$samples[[1]])) -out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins -expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)]) +if(at_home){ + ref <- readRDS("reference_parsorder.Rds") + out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins + expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)]) +} # Reordered parameter names and no DIC----------------------------------------- pars_new <- c("mu", "sigma", "alpha", "beta") out <- jags(data = data, inits = inits, parameters.to.save = pars_new, model.file = modfile, n.chains = 3, n.adapt = 100, n.iter = 100, n.burnin = 50, n.thin = 1, DIC = FALSE, verbose=FALSE) -ref <- readRDS("reference_parsorder_noDIC.Rds") +expect_equal(c(paste0("mu[",1:16,"]"), "sigma","alpha","beta"), + colnames(out$samples[[1]])) -out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins -expect_equal(out[-c(15,16,19)], ref[-c(15,16,19)]) +if(at_home){ + ref <- readRDS("reference_parsorder_noDIC.Rds") + out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins + expect_equal(out[-c(15,16,19)], ref[-c(15,16,19)]) +} # Run in parallel-------------------------------------------------------------- -at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" ) if(parallel::detectCores() > 1 & at_home){ set.seed(123) params <- c('alpha','beta','sigma', 'mu') |