diff --git a/DESCRIPTION b/DESCRIPTION
index 00206d29..94f1de34 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: rbmi
Title: Reference Based Multiple Imputation
-Version: 1.1.2
+Version: 1.1.3
Authors@R: c(
person("Craig", "Gower-Page", email = "craig.gower-page@roche.com", role = c("aut", "cre")),
person("Alessandro", "Noci", email = "alessandro.noci@roche.com", role = c("aut")),
diff --git a/R/mcmc.R b/R/mcmc.R
index 109e125f..5924df9c 100644
--- a/R/mcmc.R
+++ b/R/mcmc.R
@@ -115,6 +115,12 @@ fit_mcmc <- function(
)
)
+ assert_that(
+ !is.na(seed),
+ !is.null(seed),
+ is.numeric(seed),
+ msg = "mcmc seed is invalid"
+ )
sampling_args$seed <- seed
stan_fit <- record({
diff --git a/R/methods.R b/R/methods.R
index c5bfd959..c652cdf9 100644
--- a/R/methods.R
+++ b/R/methods.R
@@ -93,7 +93,7 @@ method_bayes <- function(
burn_between = 50,
same_cov = TRUE,
n_samples = 20,
- seed = NA
+ seed = sample.int(.Machine$integer.max, 1)
) {
x <- list(
burn_in = burn_in,
diff --git a/cran-comments.md b/cran-comments.md
index 6aea0b6d..f7398558 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,10 +1,7 @@
## Resubmission
This is a resubmission. In this version I have:
-* Stabilised some of our unit tests to reduce the occurrence of false-positive failures due to random variations from different CPU's/OS's.
-* Added a bug report URL and a support site URL to our DESCRIPTION file
-* Updated STAN code to hopefully fix the clang-UBSAN error. Please note though we were not able
-to reproduce this CRAN error locally so are not 100% if this fix will work.
+* Fixed the clang-UBSAN error
## R CMD check results
diff --git a/man/method.Rd b/man/method.Rd
index 960fc824..0ba22c87 100644
--- a/man/method.Rd
+++ b/man/method.Rd
@@ -13,7 +13,7 @@ method_bayes(
burn_between = 50,
same_cov = TRUE,
n_samples = 20,
- seed = NA
+ seed = sample.int(.Machine$integer.max, 1)
)
method_approxbayes(
diff --git a/tests/testthat/test-mcmc.R b/tests/testthat/test-mcmc.R
index 16ecbad2..581a5763 100644
--- a/tests/testthat/test-mcmc.R
+++ b/tests/testthat/test-mcmc.R
@@ -421,7 +421,8 @@ test_that("fit_mcmc can recover known values with same_cov = TRUE", {
group = dat2$group,
subjid = dat2$id,
visit = dat2$visit,
- method = method
+ method = method,
+ quiet = TRUE
)
beta_within <- get_within(fit$samples$beta, c(10, 6, 3, 7, 0, 0, 7, 14))
@@ -602,3 +603,38 @@ test_that("fit_mcmc can recover known values with same_cov = FALSE", {
})
+
+
+test_that("invalid seed throws an error", {
+
+ set.seed(301)
+ sigma <- as_vcov(c(6, 4, 4), c(0.5, 0.2, 0.3))
+ dat <- get_sim_data(50, sigma)
+
+ dat_ice <- dat %>%
+ group_by(id) %>%
+ arrange(desc(visit)) %>%
+ slice(1) %>%
+ ungroup() %>%
+ mutate(strategy = "MAR")
+
+ vars <- set_vars(
+ visit = "visit",
+ subjid = "id",
+ group = "group",
+ covariates = "sex",
+ strategy = "strategy",
+ outcome = "outcome"
+ )
+
+ expect_error(
+ draws(
+ dat,
+ dat_ice,
+ vars,
+ method_bayes(n_samples = 2, seed = NA),
+ quiet = TRUE
+ ),
+ regexp = "mcmc seed is invalid"
+ )
+})
diff --git a/vignettes/advanced.html b/vignettes/advanced.html
index be8903d3..3b4a85ca 100644
--- a/vignettes/advanced.html
+++ b/vignettes/advanced.html
@@ -15,19 +15,6 @@
rbmi: Advanced Functionality
-