Seamless update

alimacher · Aug 30, 2024 · 5216402 · 5216402
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diff --git a/.DS_Store b/.DS_Store
diff --git a/01-SampleSize-Seamless.qmd b/01-SampleSize-Seamless.qmd
@@ -0,0 +1,24 @@
+# Seamless phase-II/III study
+
+```{r}
+#| echo: false
+#| warning: false
+
+library(ggplot2)
+library(tidyverse)
+library(splitstackshape)
+library(extraDistr)
+```
+
+This vignette was motivated by a study of CTU Bern (1938). It is an example of a Bayesian seamless phase-II/III design. The primary endpoint is a binary endpoint, say, treatment discontinuation (TD).
+
+
+## Methods
+
+## Author {-}
+
+André Moser, Senior Statistician\
+Iulia-Maia Muresan, Statistician\
+Department of Clinical Research\
+University of Bern\
+3012 Bern, Switzerland
diff --git a/_quarto.yml b/_quarto.yml
@@ -15,6 +15,7 @@ book:
       chapters:	
         - 01-SampleSize-BinaryOutcome.qmd
         - 01-SampleSize-ContinuousOutcome.qmd
+        - 01-SampleSize-Seamless.qmd
         - 01-SampleSize_Bayesian_power_basics_examples.qmd
     - references.qmd
 

diff --git a/docs/01-SampleSize-BinaryOutcome.html b/docs/01-SampleSize-BinaryOutcome.html
@@ -208,11 +208,17 @@ <h1 class="title"><span class="chapter-number">1</span>&nbsp; <span class="chapt
   <a href="./01-SampleSize-ContinuousOutcome.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Two-arm study with a continuous primary outcome</span></span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./01-SampleSize-Seamless.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Seamless phase-II/III study</span></span></a>
+  </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./01-SampleSize_Bayesian_power_basics_examples.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
   </div>
 </li>
       </ul>

diff --git a/docs/01-SampleSize-ContinuousOutcome.html b/docs/01-SampleSize-ContinuousOutcome.html
@@ -59,7 +59,7 @@
 
 <script src="site_libs/quarto-nav/quarto-nav.js"></script>
 <script src="site_libs/quarto-nav/headroom.min.js"></script>
-<link href="./01-SampleSize_Bayesian_power_basics_examples.html" rel="next">
+<link href="./01-SampleSize-Seamless.html" rel="next">
 <link href="./01-SampleSize-BinaryOutcome.html" rel="prev">
 <script src="site_libs/clipboard/clipboard.min.js"></script>
 <script src="site_libs/quarto-html/quarto.js"></script>
@@ -157,11 +157,17 @@ <h1 class="title"><span class="chapter-number">2</span>&nbsp; <span class="chapt
   <a href="./01-SampleSize-ContinuousOutcome.html" class="sidebar-item-text sidebar-link active">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Two-arm study with a continuous primary outcome</span></span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./01-SampleSize-Seamless.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Seamless phase-II/III study</span></span></a>
+  </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./01-SampleSize_Bayesian_power_basics_examples.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
   </div>
 </li>
       </ul>
@@ -763,8 +769,8 @@ <h3 class="unnumbered anchored" data-anchor-id="author">Author</h3>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./01-SampleSize_Bayesian_power_basics_examples.html" class="pagination-link" aria-label="External resources and references">
-        <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">External resources and references</span></span> <i class="bi bi-arrow-right-short"></i>
+      <a href="./01-SampleSize-Seamless.html" class="pagination-link" aria-label="Seamless phase-II/III study">
+        <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Seamless phase-II/III study</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>

diff --git a/docs/02-SampleSize-ContinuousOutcome.html → docs/01-SampleSize-Seamless.html b/docs/02-SampleSize-ContinuousOutcome.html → docs/01-SampleSize-Seamless.html
diff --git a/docs/01-SampleSize.html b/docs/01-SampleSize.html
@@ -123,11 +123,17 @@ <h1 class="title">Sample size</h1>
   <a href="./01-SampleSize-ContinuousOutcome.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Two-arm study with a continuous primary outcome</span></span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./01-SampleSize-Seamless.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Seamless phase-II/III study</span></span></a>
+  </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./01-SampleSize_Bayesian_power_basics_examples.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
   </div>
 </li>
       </ul>
@@ -153,7 +159,7 @@ <h1 class="title">Sample size</h1>
 
 
 
-<p>This section covers specific the examples of the topic of ‘sample size’.</p>
+<p>This section covers specific the examples related to the topic of ‘sample size’.</p>
 
 
 

diff --git a/docs/01-SampleSize_Bayesian_power_basics_examples.html b/docs/01-SampleSize_Bayesian_power_basics_examples.html
@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Bayesian Toolbox – 3&nbsp; External resources and references</title>
+<title>Bayesian Toolbox – 4&nbsp; External resources and references</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -26,7 +26,7 @@
 <script src="site_libs/quarto-nav/quarto-nav.js"></script>
 <script src="site_libs/quarto-nav/headroom.min.js"></script>
 <link href="./references.html" rel="next">
-<link href="./01-SampleSize-ContinuousOutcome.html" rel="prev">
+<link href="./01-SampleSize-Seamless.html" rel="prev">
 <script src="site_libs/clipboard/clipboard.min.js"></script>
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
@@ -66,7 +66,7 @@
       <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" role="button" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
-        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./01-SampleSize.html">Sample size</a></li><li class="breadcrumb-item"><a href="./01-SampleSize_Bayesian_power_basics_examples.html"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">External resources and references</span></a></li></ol></nav>
+        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./01-SampleSize.html">Sample size</a></li><li class="breadcrumb-item"><a href="./01-SampleSize_Bayesian_power_basics_examples.html"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">External resources and references</span></a></li></ol></nav>
         <a class="flex-grow-1" role="navigation" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
@@ -75,8 +75,8 @@
 <!-- content -->
 <header id="title-block-header" class="quarto-title-block default toc-left page-columns page-full">
   <div class="quarto-title-banner page-columns page-full">
-    <div class="quarto-title column-body"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./01-SampleSize.html">Sample size</a></li><li class="breadcrumb-item"><a href="./01-SampleSize_Bayesian_power_basics_examples.html"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">External resources and references</span></a></li></ol></nav>
-      <h1 class="title"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">External resources and references</span></h1>
+    <div class="quarto-title column-body"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./01-SampleSize.html">Sample size</a></li><li class="breadcrumb-item"><a href="./01-SampleSize_Bayesian_power_basics_examples.html"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">External resources and references</span></a></li></ol></nav>
+      <h1 class="title"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">External resources and references</span></h1>
                       </div>
   </div>
 
@@ -123,11 +123,17 @@ <h1 class="title"><span class="chapter-number">3</span>&nbsp; <span class="chapt
   <a href="./01-SampleSize-ContinuousOutcome.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Two-arm study with a continuous primary outcome</span></span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./01-SampleSize-Seamless.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Seamless phase-II/III study</span></span></a>
+  </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./01-SampleSize_Bayesian_power_basics_examples.html" class="sidebar-item-text sidebar-link active">
- <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
   </div>
 </li>
       </ul>
@@ -144,9 +150,9 @@ <h1 class="title"><span class="chapter-number">3</span>&nbsp; <span class="chapt
     <h2 id="toc-title">Table of contents</h2>
 
   <ul>
-  <li><a href="#peer-reviewed-articles" id="toc-peer-reviewed-articles" class="nav-link active" data-scroll-target="#peer-reviewed-articles"><span class="header-section-number">3.1</span> Peer-reviewed articles</a></li>
-  <li><a href="#blog-posts" id="toc-blog-posts" class="nav-link" data-scroll-target="#blog-posts"><span class="header-section-number">3.2</span> Blog posts</a></li>
-  <li><a href="#r-packages-and-online-tools" id="toc-r-packages-and-online-tools" class="nav-link" data-scroll-target="#r-packages-and-online-tools"><span class="header-section-number">3.3</span> R packages and online tools</a></li>
+  <li><a href="#peer-reviewed-articles" id="toc-peer-reviewed-articles" class="nav-link active" data-scroll-target="#peer-reviewed-articles"><span class="header-section-number">4.1</span> Peer-reviewed articles</a></li>
+  <li><a href="#blog-posts" id="toc-blog-posts" class="nav-link" data-scroll-target="#blog-posts"><span class="header-section-number">4.2</span> Blog posts</a></li>
+  <li><a href="#r-packages-and-online-tools" id="toc-r-packages-and-online-tools" class="nav-link" data-scroll-target="#r-packages-and-online-tools"><span class="header-section-number">4.3</span> R packages and online tools</a></li>
   <li><a href="#author" id="toc-author" class="nav-link" data-scroll-target="#author">Author</a></li>
   </ul>
 </nav>
@@ -162,8 +168,8 @@ <h2 id="toc-title">Table of contents</h2>
 
 
 
-<section id="peer-reviewed-articles" class="level2" data-number="3.1">
-<h2 data-number="3.1" class="anchored" data-anchor-id="peer-reviewed-articles"><span class="header-section-number">3.1</span> Peer-reviewed articles</h2>
+<section id="peer-reviewed-articles" class="level2" data-number="4.1">
+<h2 data-number="4.1" class="anchored" data-anchor-id="peer-reviewed-articles"><span class="header-section-number">4.1</span> Peer-reviewed articles</h2>
 <ul>
 <li><p>A Review of Bayesian Perspectives on Sample Size Derivation for Confirmatory Trials (2021).<br>
 <a href="https://pubmed.ncbi.nlm.nih.gov/34992303/" class="uri">https://pubmed.ncbi.nlm.nih.gov/34992303/</a></p></li>
@@ -175,8 +181,8 @@ <h2 data-number="3.1" class="anchored" data-anchor-id="peer-reviewed-articles"><
 <li><p>Bayesian and mixed bayesian/likelihood criteria for sample size determination <a href="https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0258(19970415)16:7%3C769::AID-SIM495%3E3.0.CO;2-V" class="uri">https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0258(19970415)16:7%3C769::AID-SIM495%3E3.0.CO;2-V</a></p></li>
 </ul>
 </section>
-<section id="blog-posts" class="level2" data-number="3.2">
-<h2 data-number="3.2" class="anchored" data-anchor-id="blog-posts"><span class="header-section-number">3.2</span> Blog posts</h2>
+<section id="blog-posts" class="level2" data-number="4.2">
+<h2 data-number="4.2" class="anchored" data-anchor-id="blog-posts"><span class="header-section-number">4.2</span> Blog posts</h2>
 <ul>
 <li><p>Introduction to bayesian clinical trial designs (detailed - including R code examples)<br>
 <a href="https://hbiostat.org/bayes/bet/design" class="uri">https://hbiostat.org/bayes/bet/design</a></p></li>
@@ -188,8 +194,8 @@ <h2 data-number="3.2" class="anchored" data-anchor-id="blog-posts"><span class="
 <li><p>Stopping rules using bayesian analyses <a href="https://statmodeling.stat.columbia.edu/2014/02/13/stopping-rules-bayesian-analysis/" class="uri">https://statmodeling.stat.columbia.edu/2014/02/13/stopping-rules-bayesian-analysis/</a> <a href="http://varianceexplained.org/r/bayesian-ab-testing/" class="uri">http://varianceexplained.org/r/bayesian-ab-testing/</a></p></li>
 </ul>
 </section>
-<section id="r-packages-and-online-tools" class="level2" data-number="3.3">
-<h2 data-number="3.3" class="anchored" data-anchor-id="r-packages-and-online-tools"><span class="header-section-number">3.3</span> R packages and online tools</h2>
+<section id="r-packages-and-online-tools" class="level2" data-number="4.3">
+<h2 data-number="4.3" class="anchored" data-anchor-id="r-packages-and-online-tools"><span class="header-section-number">4.3</span> R packages and online tools</h2>
 <ul>
 <li><p><strong>Package ‘SampleSizeProportions’ (2023)</strong><br>
 Calculating Sample Size Requirements when Estimating the Difference Between Two Binomial Proportions <a href="https://cran.rstudio.com/web/packages/SampleSizeProportions/index.html" class="uri">https://cran.rstudio.com/web/packages/SampleSizeProportions/index.html</a></p></li>
@@ -638,8 +644,8 @@ <h2 class="unnumbered anchored" data-anchor-id="author">Author</h2>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="./01-SampleSize-ContinuousOutcome.html" class="pagination-link" aria-label="Two-arm study with a continuous primary outcome">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Two-arm study with a continuous primary outcome</span></span>
+      <a href="./01-SampleSize-Seamless.html" class="pagination-link" aria-label="Seamless phase-II/III study">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Seamless phase-II/III study</span></span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">

diff --git a/docs/index.html b/docs/index.html
@@ -122,11 +122,17 @@ <h1 class="title">Bayesian Toolbox</h1>
   <a href="./01-SampleSize-ContinuousOutcome.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Two-arm study with a continuous primary outcome</span></span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./01-SampleSize-Seamless.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Seamless phase-II/III study</span></span></a>
+  </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./01-SampleSize_Bayesian_power_basics_examples.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
   </div>
 </li>
       </ul>

diff --git a/docs/references.html b/docs/references.html
@@ -141,11 +141,17 @@ <h1 class="title">References</h1>
   <a href="./01-SampleSize-ContinuousOutcome.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Two-arm study with a continuous primary outcome</span></span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./01-SampleSize-Seamless.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Seamless phase-II/III study</span></span></a>
+  </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./01-SampleSize_Bayesian_power_basics_examples.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">External resources and references</span></span></a>
   </div>
 </li>
       </ul>
@@ -610,7 +616,7 @@ <h1 class="title">References</h1>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
       <a href="./01-SampleSize_Bayesian_power_basics_examples.html" class="pagination-link" aria-label="External resources and references">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">External resources and references</span></span>
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">External resources and references</span></span>
       </a>          
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