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Fixes for JAGS 5.0.0 #56

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Merged
kenkellner merged 1 commit into from
Jan 7, 2026
Merged

Fixes for JAGS 5.0.0 #56

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ Imports:
graphics,
grDevices,
parallel,
rjags (>= 3-13),
rjags (>= 4-17),
stats,
utils
Suggests: knitr, markdown, tinytest
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8 changes: 7 additions & 1 deletion R/run_rjags.R
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Expand Up @@ -281,7 +281,13 @@ set.factories <- function(factories){
set.modules <- function(modules,DIC){

#Load/unload appropriate modules (besides dic)
called.set <- c('basemod','bugs',modules)

default.set <- c('basemod', 'bugs')
if (rjags::jags.version() >= as.numeric_version("5")) {
#deviance monitor moved to the 'diag' module so load by default
default.set <- c(default.set, 'diag')
}
called.set <- c(default.set, modules)
current.set <- rjags::list.modules()

load.set <- called.set[!called.set%in%current.set]
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17 changes: 13 additions & 4 deletions inst/tinytest/test_autojags.R
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Expand Up @@ -71,10 +71,19 @@ nul <- capture.output(

# Runs three updates of 10 iterations each
expect_true(grepl("Note: ALL iterations", nul[6]))
expect_true(grepl("Update 3", nul[10]))
expect_true(nul[11] == "")
# All are combined to yield 30 total iterations in each chain
expect_equal(coda::niter(out$samples), 30)
if (rjags::jags.version() >= as.numeric_version("5")) {
expect_true(grepl("Update 2", nul[9]))
expect_true(nul[10] == "")
# All are combined to yield 20 total iterations in each chain
expect_equal(coda::niter(out$samples), 20)

} else {
expect_true(grepl("Update 3", nul[10]))
expect_true(nul[11] == "")
# All are combined to yield 30 total iterations in each chain
expect_equal(coda::niter(out$samples), 30)
}


if(at_home){
ref <- readRDS("autojags_ref_alliter.Rds")
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30 changes: 18 additions & 12 deletions inst/tinytest/test_run_rjags.R
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@@ -1,22 +1,28 @@
# load_modules loads and unloads correctly

if (rjags::jags.version() < as.numeric_version("5")) {
default.modules <- c('basemod','bugs')
test.factories <- 1:2
} else {
default.modules <- c('basemod','bugs','diag') # diag provides deviance monitor
test.factories <- c(6,1) # change in precedence of bugs::binomSlice factory
}

jagsUI:::set.modules(NULL, FALSE)
expect_equal(rjags::list.modules(),c('basemod','bugs'))
expect_equal(rjags::list.modules(),default.modules)
jagsUI:::set.modules('glm', FALSE)
expect_equal(rjags::list.modules(),c('basemod','bugs','glm'))
expect_equal(rjags::list.modules(),c(default.modules,'glm'))
jagsUI:::set.modules(NULL, FALSE)
expect_equal(rjags::list.modules(),c('basemod','bugs'))
expect_equal(rjags::list.modules(),default.modules)
jagsUI:::set.modules(NULL, DIC=TRUE)
expect_equal(rjags::list.modules(),c('basemod','bugs','dic'))

expect_equal(rjags::list.modules(),c(default.modules,'dic'))

# load_factories works correctly
jagsUI:::set.factories(NULL)
expect_equal(rjags::list.factories('sampler')[1:2,2], c(TRUE, TRUE))
jagsUI:::set.factories(c('bugs::BinomSlice sampler FALSE',
'bugs::RW1 sampler FALSE'))
expect_equal(rjags::list.factories('sampler')[1:2,2], c(FALSE, FALSE))
jagsUI:::set.factories(c('bugs::BinomSlice sampler TRUE',
'bugs::RW1 sampler TRUE'))
expect_equal(rjags::list.factories('sampler')[1:2,2], c(TRUE, TRUE))
expect_equal(rjags::list.factories('sampler')[test.factories,2], c(TRUE, TRUE))
jagsUI:::set.factories(c('bugs::BinomSlice sampler FALSE', 'bugs::RW1 sampler FALSE'))
expect_equal(rjags::list.factories('sampler')[test.factories,2], c(FALSE, FALSE))
jagsUI:::set.factories(c('bugs::BinomSlice sampler TRUE', 'bugs::RW1 sampler TRUE'))
expect_equal(rjags::list.factories('sampler')[test.factories,2], c(TRUE, TRUE))
expect_error(jagsUI:::set.factories(c('bad bad')))
expect_error(jagsUI:::set.factories(c('bugs::fake sampler FALSE')))
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