Merge pull request #335 from insightsengineering/fix-stan-seed

Fix stan seed

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 = "[email protected]", role = c("aut", "cre")),
     person("Alessandro", "Noci", email = "[email protected]", role = c("aut")),

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({

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,

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
 

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"
+    )
+})

vignettes/advanced.html

@@ -15,19 +15,6 @@
 
 <title>rbmi: Advanced Functionality</title>
 
-<script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
-</script>
 
 <style type="text/css">
   code{white-space: pre-wrap;}
@@ -787,7 +774,7 @@ <h1><span class="header-section-number">6</span> Custom imputation strategies</h
 <span id="cb9-17"><a href="#cb9-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     pars &lt;- list(mu = mu, sigma = sigma)</span></span>
 <span id="cb9-18"><a href="#cb9-18" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     return(pars)</span></span>
 <span id="cb9-19"><a href="#cb9-19" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; }</span></span>
-<span id="cb9-20"><a href="#cb9-20" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;bytecode: 0x7f9546ca2148&gt;</span></span>
+<span id="cb9-20"><a href="#cb9-20" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;bytecode: 0x7ff3aeaeb098&gt;</span></span>
 <span id="cb9-21"><a href="#cb9-21" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;environment: namespace:rbmi&gt;</span></span></code></pre></div>
 <p>To further illustrate this for a simple example, assume that a new strategy is to be implemented as follows:
 - The marginal mean of the imputation distribution is equal to the marginal mean trajectory for the subject according to their assigned group and covariates up to the ICE.

vignettes/quickstart.html

@@ -15,19 +15,6 @@
 
 <title>rbmi: Quickstart</title>
 
-<script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
-</script>
 
 <style type="text/css">
   code{white-space: pre-wrap;}
@@ -474,7 +461,7 @@ <h1><span class="header-section-number">3</span> Draws</h1>
 <span id="cb3-71"><a href="#cb3-71" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     burn_between: 5</span></span>
 <span id="cb3-72"><a href="#cb3-72" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     same_cov: TRUE</span></span>
 <span id="cb3-73"><a href="#cb3-73" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     n_samples: 150</span></span>
-<span id="cb3-74"><a href="#cb3-74" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     seed: NA</span></span></code></pre></div>
+<span id="cb3-74"><a href="#cb3-74" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     seed: 373388384</span></span></code></pre></div>
 <p>Note the use of <code>set_vars()</code> which specifies the names of the key variables
 within the dataset and the imputation model. Additionally, note that whilst <code>vars$group</code> and <code>vars$visit</code>
 are added as terms to the imputation model by default, their interaction is not,
@@ -699,34 +686,34 @@ <h1><span class="header-section-number">6</span> Pool</h1>
 <span id="cb8-20"><a href="#cb8-20" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;      trt_4    -0.092  0.683  -1.439  1.256   0.893  </span></span>
 <span id="cb8-21"><a href="#cb8-21" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_ref_4  -1.616  0.486  -2.576  -0.656  0.001  </span></span>
 <span id="cb8-22"><a href="#cb8-22" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_alt_4  -1.708  0.475  -2.645  -0.77   &lt;0.001 </span></span>
-<span id="cb8-23"><a href="#cb8-23" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;      trt_5     1.34   0.925  -0.486  3.166   0.149  </span></span>
-<span id="cb8-24"><a href="#cb8-24" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_ref_5  -4.154  0.66   -5.457  -2.852  &lt;0.001 </span></span>
-<span id="cb8-25"><a href="#cb8-25" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_alt_5  -2.815  0.647  -4.092  -1.538  &lt;0.001 </span></span>
-<span id="cb8-26"><a href="#cb8-26" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;      trt_6    1.956   0.999  -0.018  3.931   0.052  </span></span>
-<span id="cb8-27"><a href="#cb8-27" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_ref_6   -6.1   0.72   -7.523  -4.678  &lt;0.001 </span></span>
-<span id="cb8-28"><a href="#cb8-28" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_alt_6  -4.144  0.695  -5.516  -2.772  &lt;0.001 </span></span>
-<span id="cb8-29"><a href="#cb8-29" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;      trt_7    2.178   1.124  -0.043  4.399   0.055  </span></span>
-<span id="cb8-30"><a href="#cb8-30" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_ref_7  -7.001  0.822  -8.628  -5.375  &lt;0.001 </span></span>
-<span id="cb8-31"><a href="#cb8-31" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_alt_7  -4.823  0.789  -6.384  -3.263  &lt;0.001 </span></span>
+<span id="cb8-23"><a href="#cb8-23" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;      trt_5    1.317   0.931  -0.522  3.156   0.159  </span></span>
+<span id="cb8-24"><a href="#cb8-24" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_ref_5  -4.141  0.661  -5.446  -2.836  &lt;0.001 </span></span>
+<span id="cb8-25"><a href="#cb8-25" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_alt_5  -2.823  0.647  -4.102  -1.545  &lt;0.001 </span></span>
+<span id="cb8-26"><a href="#cb8-26" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;      trt_6    1.919   1.006  -0.069  3.907   0.058  </span></span>
+<span id="cb8-27"><a href="#cb8-27" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_ref_6  -6.087  0.718  -7.505  -4.668  &lt;0.001 </span></span>
+<span id="cb8-28"><a href="#cb8-28" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_alt_6  -4.168  0.703  -5.558  -2.778  &lt;0.001 </span></span>
+<span id="cb8-29"><a href="#cb8-29" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;      trt_7    2.132   1.133  -0.107  4.372   0.062  </span></span>
+<span id="cb8-30"><a href="#cb8-30" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_ref_7  -6.945  0.837  -8.602  -5.288  &lt;0.001 </span></span>
+<span id="cb8-31"><a href="#cb8-31" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    lsm_alt_7  -4.813  0.789  -6.373  -3.253  &lt;0.001 </span></span>
 <span id="cb8-32"><a href="#cb8-32" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   --------------------------------------------------</span></span></code></pre></div>
 <p>The table of values shown in the print message for <code>poolObj</code> can also be extracted using the <code>as.data.frame()</code> function:</p>
 <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">as.data.frame</span>(poolObj)</span>
 <span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;    parameter         est        se         lci        uci         pval</span></span>
 <span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1      trt_4 -0.09180645 0.6826279 -1.43949684  1.2558839 8.931772e-01</span></span>
 <span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2  lsm_ref_4 -1.61581996 0.4862316 -2.57577141 -0.6558685 1.093708e-03</span></span>
 <span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3  lsm_alt_4 -1.70762640 0.4749573 -2.64531931 -0.7699335 4.262148e-04</span></span>
-<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4      trt_5  1.33975256 0.9245536 -0.48627442  3.1657795 1.492897e-01</span></span>
-<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 5  lsm_ref_5 -4.15439612 0.6596139 -5.45719295 -2.8515993 2.853288e-09</span></span>
-<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 6  lsm_alt_5 -2.81464355 0.6465855 -4.09178487 -1.5375022 2.412198e-05</span></span>
-<span id="cb9-9"><a href="#cb9-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 7      trt_6  1.95633775 0.9994792 -0.01823149  3.9309070 5.212617e-02</span></span>
-<span id="cb9-10"><a href="#cb9-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 8  lsm_ref_6 -6.10037936 0.7197954 -7.52269771 -4.6780610 2.097471e-14</span></span>
-<span id="cb9-11"><a href="#cb9-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 9  lsm_alt_6 -4.14404161 0.6946859 -5.51643551 -2.7716477 1.625003e-08</span></span>
-<span id="cb9-12"><a href="#cb9-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 10     trt_7  2.17794477 1.1237356 -0.04320821  4.3990977 5.456450e-02</span></span>
-<span id="cb9-13"><a href="#cb9-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 11 lsm_ref_7 -7.00142993 0.8223970 -8.62790047 -5.3749594 2.911670e-14</span></span>
-<span id="cb9-14"><a href="#cb9-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 12 lsm_alt_7 -4.82348516 0.7893734 -6.38405217 -3.2629182 9.210812e-09</span></span></code></pre></div>
+<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4      trt_5  1.31716908 0.9309119 -0.52157744  3.1559156 1.590740e-01</span></span>
+<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 5  lsm_ref_5 -4.14060567 0.6607424 -5.44563157 -2.8355798 3.357886e-09</span></span>
+<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 6  lsm_alt_5 -2.82343659 0.6473700 -4.10211675 -1.5447564 2.330587e-05</span></span>
+<span id="cb9-9"><a href="#cb9-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 7      trt_6  1.91890493 1.0061776 -0.06905222  3.9068621 5.839789e-02</span></span>
+<span id="cb9-10"><a href="#cb9-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 8  lsm_ref_6 -6.08671772 0.7179474 -7.50524961 -4.6681858 1.941623e-14</span></span>
+<span id="cb9-11"><a href="#cb9-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 9  lsm_alt_6 -4.16781280 0.7033519 -5.55758309 -2.7780425 2.053928e-08</span></span>
+<span id="cb9-12"><a href="#cb9-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 10     trt_7  2.13242993 1.1328896 -0.10700795  4.3718678 6.183489e-02</span></span>
+<span id="cb9-13"><a href="#cb9-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 11 lsm_ref_7 -6.94503554 0.8373644 -8.60163962 -5.2884315 1.191826e-13</span></span>
+<span id="cb9-14"><a href="#cb9-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 12 lsm_alt_7 -4.81260561 0.7891469 -6.37258775 -3.2526235 9.589554e-09</span></span></code></pre></div>
 <p>These outputs gives an estimated difference of
-2.178 (95% CI -0.043 to 4.399)
-between the two groups at the last visit with an associated p-value of 0.055.</p>
+2.132 (95% CI -0.107 to 4.372)
+between the two groups at the last visit with an associated p-value of 0.062.</p>
 </div>
 <div id="code" class="section level1" number="7">
 <h1><span class="header-section-number">7</span> Code</h1>

vignettes/stat_specs.html

@@ -15,19 +15,6 @@
 
 <title>rbmi: Statistical Specifications</title>
 
-<script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
-</script>
 
 <style type="text/css">
   code{white-space: pre-wrap;}