Deploying to gh-pages from @ 42cfa4b 🚀

index.html

@@ -10,7 +10,7 @@
 <meta name="author" content="Björn Holzhauer - [email protected]">
 <meta name="author" content="Lukas Widmer - [email protected]">
 <meta name="author" content="Andrew Bean - [email protected]">
-<meta name="dcterms.date" content="2024-04-18">
+<meta name="dcterms.date" content="2024-04-19">
 
 <title>(Bayesian) Applied Modelling in Drug Development (BAMDD)</title>
 <style>
@@ -303,7 +303,7 @@ <h2 id="toc-title">Table of contents</h2>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">April 18, 2024</p>
+      <p class="date">April 19, 2024</p>
     </div>
   </div>
 

sitemap.xml

@@ -2,58 +2,58 @@
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   <url>
     <loc>https://opensource.nibr.com/RBesT/index.html</loc>
-    <lastmod>2024-04-18T18:57:00.885Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.399Z</lastmod>
   </url>
   <url>
     <loc>https://opensource.nibr.com/RBesT/src/01a_introduction.html</loc>
-    <lastmod>2024-04-18T18:57:00.893Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.403Z</lastmod>
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   <url>
     <loc>https://opensource.nibr.com/RBesT/src/01b_basic_workflow.html</loc>
-    <lastmod>2024-04-18T18:57:00.893Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.403Z</lastmod>
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   <url>
     <loc>https://opensource.nibr.com/RBesT/src/02_case_studies.html</loc>
-    <lastmod>2024-04-18T18:57:00.893Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.403Z</lastmod>
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   <url>
     <loc>https://opensource.nibr.com/RBesT/src/02a_meta_analysis.html</loc>
-    <lastmod>2024-04-18T18:57:00.893Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.403Z</lastmod>
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   <url>
     <loc>https://opensource.nibr.com/RBesT/src/02ab_meta_analysis_trtdiff.html</loc>
-    <lastmod>2024-04-18T18:57:00.893Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.403Z</lastmod>
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   <url>
     <loc>https://opensource.nibr.com/RBesT/src/02b_dose_finding.html</loc>
-    <lastmod>2024-04-18T18:57:00.893Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.403Z</lastmod>
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   <url>
     <loc>https://opensource.nibr.com/RBesT/src/02c_dose_escalation.html</loc>
-    <lastmod>2024-04-18T18:57:00.893Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.403Z</lastmod>
   </url>
   <url>
     <loc>https://opensource.nibr.com/RBesT/src/02e_multiple_imputation.html</loc>
-    <lastmod>2024-04-18T18:57:00.893Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.403Z</lastmod>
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   <url>
     <loc>https://opensource.nibr.com/RBesT/src/02h_mmrm.html</loc>
-    <lastmod>2024-04-18T18:57:00.897Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.407Z</lastmod>
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   <url>
     <loc>https://opensource.nibr.com/RBesT/src/02i_time_to_event.html</loc>
-    <lastmod>2024-04-18T18:57:00.897Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.407Z</lastmod>
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   <url>
     <loc>https://opensource.nibr.com/RBesT/src/02j_network_meta_analysis.html</loc>
-    <lastmod>2024-04-18T18:57:00.897Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.407Z</lastmod>
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   <url>
     <loc>https://opensource.nibr.com/RBesT/src/03a_stan_code.html</loc>
-    <lastmod>2024-04-18T18:57:00.897Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.407Z</lastmod>
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     <loc>https://opensource.nibr.com/RBesT/src/03b_parallel.html</loc>
-    <lastmod>2024-04-18T18:57:00.897Z</lastmod>
+    <lastmod>2024-04-18T22:31:52.407Z</lastmod>
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src/01b_basic_workflow.html

@@ -680,7 +680,7 @@ <h2 data-number="2.5" class="anchored" data-anchor-id="fitting-the-model"><span
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 4 sequential chains...
 
-Chain 1 finished in 0.2 seconds.
+Chain 1 finished in 0.1 seconds.
 Chain 2 finished in 0.1 seconds.
 Chain 3 finished in 0.1 seconds.
 Chain 4 finished in 0.1 seconds.
@@ -821,9 +821,9 @@ <h2 data-number="2.6" class="anchored" data-anchor-id="model-summary"><span clas
 <pre><code>Running MCMC with 4 sequential chains...
 
 Chain 1 finished in 0.0 seconds.
-Chain 2 finished in 0.1 seconds.
+Chain 2 finished in 0.0 seconds.
 Chain 3 finished in 0.0 seconds.
-Chain 4 finished in 0.1 seconds.
+Chain 4 finished in 0.0 seconds.
 
 All 4 chains finished successfully.
 Mean chain execution time: 0.0 seconds.

src/02b_dose_finding.html

@@ -852,35 +852,35 @@ <h3 data-number="5.6.3" class="anchored" data-anchor-id="perform-bayesian-model-
 <pre><code>Running MCMC with 4 sequential chains...
 
 Chain 1 finished in 0.6 seconds.
-Chain 2 finished in 0.8 seconds.
+Chain 2 finished in 0.7 seconds.
 Chain 3 finished in 0.8 seconds.
 Chain 4 finished in 0.8 seconds.
 
 All 4 chains finished successfully.
 Mean chain execution time: 0.7 seconds.
-Total execution time: 3.3 seconds.
+Total execution time: 3.2 seconds.
 
 Running MCMC with 4 sequential chains...
 
 Chain 1 finished in 0.3 seconds.
 Chain 2 finished in 0.2 seconds.
 Chain 3 finished in 0.3 seconds.
-Chain 4 finished in 0.5 seconds.
+Chain 4 finished in 0.4 seconds.
 
 All 4 chains finished successfully.
 Mean chain execution time: 0.3 seconds.
-Total execution time: 1.8 seconds.
+Total execution time: 1.5 seconds.
 
 Running MCMC with 4 sequential chains...
 
 Chain 1 finished in 0.2 seconds.
 Chain 2 finished in 0.4 seconds.
-Chain 3 finished in 0.4 seconds.
+Chain 3 finished in 0.3 seconds.
 Chain 4 finished in 0.3 seconds.
 
 All 4 chains finished successfully.
 Mean chain execution time: 0.3 seconds.
-Total execution time: 1.8 seconds.
+Total execution time: 1.6 seconds.
 
 Running MCMC with 4 sequential chains...
 
@@ -917,7 +917,7 @@ <h3 data-number="5.6.3" class="anchored" data-anchor-id="perform-bayesian-model-
 
 Running MCMC with 4 sequential chains...
 
-Chain 1 finished in 0.3 seconds.
+Chain 1 finished in 0.2 seconds.
 Chain 2 finished in 0.3 seconds.
 Chain 3 finished in 0.3 seconds.
 Chain 4 finished in 0.2 seconds.

src/02e_multiple_imputation.html

@@ -616,14 +616,14 @@ <h3 data-number="7.5.1" class="anchored" data-anchor-id="imputation-from-observe
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 4 sequential chains...
 
-Chain 1 finished in 11.3 seconds.
+Chain 1 finished in 11.2 seconds.
 Chain 2 finished in 10.6 seconds.
-Chain 3 finished in 13.7 seconds.
-Chain 4 finished in 13.2 seconds.
+Chain 3 finished in 13.5 seconds.
+Chain 4 finished in 13.1 seconds.
 
 All 4 chains finished successfully.
-Mean chain execution time: 12.2 seconds.
-Total execution time: 49.2 seconds.</code></pre>
+Mean chain execution time: 12.1 seconds.
+Total execution time: 48.7 seconds.</code></pre>
 </div>
 <div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Predictions for missing (lost-to-follow-up) post-treatment values</span></span>
 <span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="co"># Output format is a matrix with each column being a patient record and each row being one imputation</span></span>
@@ -667,14 +667,14 @@ <h3 data-number="7.5.2" class="anchored" data-anchor-id="imputation-based-on-the
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 4 sequential chains...
 
-Chain 1 finished in 10.3 seconds.
-Chain 2 finished in 10.2 seconds.
-Chain 3 finished in 12.9 seconds.
-Chain 4 finished in 12.3 seconds.
+Chain 1 finished in 10.1 seconds.
+Chain 2 finished in 10.1 seconds.
+Chain 3 finished in 12.8 seconds.
+Chain 4 finished in 12.1 seconds.
 
 All 4 chains finished successfully.
-Mean chain execution time: 11.4 seconds.
-Total execution time: 46.3 seconds.</code></pre>
+Mean chain execution time: 11.3 seconds.
+Total execution time: 45.5 seconds.</code></pre>
 </div>
 <div class="sourceCode cell-code" id="cb10"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>imputations2 <span class="ot">&lt;-</span> <span class="fu">predict</span>(brmfit2, </span>
 <span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a>                        <span class="at">newdata=</span>count_data <span class="sc">%&gt;%</span> </span>
@@ -712,14 +712,14 @@ <h3 data-number="7.5.3" class="anchored" data-anchor-id="imputation-under-a-hypo
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 4 sequential chains...
 
-Chain 1 finished in 12.6 seconds.
-Chain 2 finished in 9.7 seconds.
-Chain 3 finished in 10.4 seconds.
-Chain 4 finished in 13.0 seconds.
+Chain 1 finished in 12.4 seconds.
+Chain 2 finished in 9.6 seconds.
+Chain 3 finished in 10.2 seconds.
+Chain 4 finished in 12.8 seconds.
 
 All 4 chains finished successfully.
-Mean chain execution time: 11.4 seconds.
-Total execution time: 46.0 seconds.</code></pre>
+Mean chain execution time: 11.3 seconds.
+Total execution time: 45.4 seconds.</code></pre>
 </div>
 <div class="sourceCode cell-code" id="cb14"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>imputations3 <span class="ot">&lt;-</span> <span class="fu">predict</span>(brmfit3, </span>
 <span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a>                        <span class="at">newdata=</span>count_data <span class="sc">%&gt;%</span> </span>

src/02i_time_to_event.html

@@ -598,14 +598,14 @@ <h3 data-number="9.4.1" class="anchored" data-anchor-id="historical-data"><span
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 4 sequential chains...
 
-Chain 1 finished in 1.5 seconds.
+Chain 1 finished in 1.3 seconds.
 Chain 2 finished in 1.4 seconds.
 Chain 3 finished in 1.4 seconds.
 Chain 4 finished in 1.3 seconds.
 
 All 4 chains finished successfully.
-Mean chain execution time: 1.4 seconds.
-Total execution time: 5.9 seconds.</code></pre>
+Mean chain execution time: 1.3 seconds.
+Total execution time: 5.7 seconds.</code></pre>
 </div>
 <div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>fit_hist_checkmate</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
@@ -3512,12 +3512,12 @@ <h3 data-number="9.6.2" class="anchored" data-anchor-id="model-fit-with-brms"><s
 
 Chain 1 finished in 0.5 seconds.
 Chain 2 finished in 0.6 seconds.
-Chain 3 finished in 0.6 seconds.
+Chain 3 finished in 0.5 seconds.
 Chain 4 finished in 0.5 seconds.
 
 All 4 chains finished successfully.
 Mean chain execution time: 0.5 seconds.
-Total execution time: 2.7 seconds.</code></pre>
+Total execution time: 2.6 seconds.</code></pre>
 </div>
 </div>
 <p>When looking at the model summary, it is preferable to use <code>robust=TRUE</code> to get the median estimate of the posterior rather than the mean (which would change due to transforms)</p>
@@ -4660,14 +4660,14 @@ <h3 data-number="9.6.3" class="anchored" data-anchor-id="incoporate-simulated-hi
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 4 sequential chains...
 
-Chain 1 finished in 1.8 seconds.
+Chain 1 finished in 1.7 seconds.
 Chain 2 finished in 1.8 seconds.
 Chain 3 finished in 1.7 seconds.
-Chain 4 finished in 1.9 seconds.
+Chain 4 finished in 1.8 seconds.
 
 All 4 chains finished successfully.
 Mean chain execution time: 1.8 seconds.
-Total execution time: 7.5 seconds.</code></pre>
+Total execution time: 7.4 seconds.</code></pre>
 </div>
 </div>
 <p>And we can compare the results from two models. Inclusion of historical data on <code>controlChemoA</code> affect the estimates of coefficients for overall mean and <code>EffectAverage</code>.</p>
@@ -4733,14 +4733,14 @@ <h3 data-number="9.6.3" class="anchored" data-anchor-id="incoporate-simulated-hi
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 4 sequential chains...
 
-Chain 1 finished in 1.3 seconds.
+Chain 1 finished in 1.2 seconds.
 Chain 2 finished in 1.1 seconds.
 Chain 3 finished in 1.2 seconds.
 Chain 4 finished in 1.1 seconds.
 
 All 4 chains finished successfully.
-Mean chain execution time: 1.2 seconds.
-Total execution time: 5.1 seconds.</code></pre>
+Mean chain execution time: 1.1 seconds.
+Total execution time: 4.9 seconds.</code></pre>
 </div>
 <div class="sourceCode cell-code" id="cb53"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb53-1"><a href="#cb53-1" aria-hidden="true" tabindex="-1"></a><span class="fu">gt</span>(<span class="fu">as.data.frame</span>(<span class="fu">fixef</span>(fit_mac_prior_weibull, <span class="at">robust=</span><span class="cn">TRUE</span>))) <span class="sc">%&gt;%</span> <span class="fu">fmt_number</span>(<span class="fu">everything</span>(), <span class="at">decimals=</span><span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output-display">
@@ -6337,8 +6337,8 @@ <h3 data-number="9.6.4" class="anchored" data-anchor-id="including-historical-da
 Chain 4 finished in 1.7 seconds.
 
 All 4 chains finished successfully.
-Mean chain execution time: 1.8 seconds.
-Total execution time: 7.3 seconds.</code></pre>
+Mean chain execution time: 1.7 seconds.
+Total execution time: 7.2 seconds.</code></pre>
 </div>
 <div class="sourceCode cell-code" id="cb60"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb60-1"><a href="#cb60-1" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(fit_mac_weibull, <span class="at">prob=</span><span class="fl">0.9</span>, <span class="at">robust=</span><span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
@@ -6442,14 +6442,14 @@ <h3 data-number="9.6.4" class="anchored" data-anchor-id="including-historical-da
 <div class="cell-output cell-output-stdout">
 <pre><code>Running MCMC with 4 sequential chains...
 
-Chain 1 finished in 6.4 seconds.
-Chain 2 finished in 6.5 seconds.
-Chain 3 finished in 6.4 seconds.
-Chain 4 finished in 6.2 seconds.
+Chain 1 finished in 6.3 seconds.
+Chain 2 finished in 6.4 seconds.
+Chain 3 finished in 6.3 seconds.
+Chain 4 finished in 6.1 seconds.
 
 All 4 chains finished successfully.
-Mean chain execution time: 6.4 seconds.
-Total execution time: 25.9 seconds.</code></pre>
+Mean chain execution time: 6.3 seconds.
+Total execution time: 25.4 seconds.</code></pre>
 </div>
 <div class="sourceCode cell-code" id="cb74"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb74-1"><a href="#cb74-1" aria-hidden="true" tabindex="-1"></a>fit_mac_weibull_ind</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">