From ab4d07eb875ea72b577fe9f1bb5d6faf31464ed6 Mon Sep 17 00:00:00 2001
From: martyn <martyn.plummer@gmail.com>
Date: Mon, 5 Jan 2026 09:55:11 +0000
Subject: [PATCH] Fixes for JAGS 5.0.0

---
 DESCRIPTION                    |  2 +-
 R/run_rjags.R                  |  8 +++++++-
 inst/tinytest/test_autojags.R  | 17 +++++++++++++----
 inst/tinytest/test_run_rjags.R | 30 ++++++++++++++++++------------
 4 files changed, 39 insertions(+), 18 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7d6902f..c589cbc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -13,7 +13,7 @@ Imports:
     graphics,
     grDevices,
     parallel,
-    rjags (>= 3-13),
+    rjags (>= 4-17),
     stats,
     utils
 Suggests: knitr, markdown, tinytest
diff --git a/R/run_rjags.R b/R/run_rjags.R
index 0b107f4..db12e13 100644
--- a/R/run_rjags.R
+++ b/R/run_rjags.R
@@ -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]
diff --git a/inst/tinytest/test_autojags.R b/inst/tinytest/test_autojags.R
index 61ff997..1b78c4f 100644
--- a/inst/tinytest/test_autojags.R
+++ b/inst/tinytest/test_autojags.R
@@ -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")
diff --git a/inst/tinytest/test_run_rjags.R b/inst/tinytest/test_run_rjags.R
index 65d05da..b42f217 100644
--- a/inst/tinytest/test_run_rjags.R
+++ b/inst/tinytest/test_run_rjags.R
@@ -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')))