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diff --git a/docs/404.html b/docs/404.html
@@ -116,7 +116,7 @@ <h1>Page not found<a class="anchor" aria-label="anchor" href="#page-not-found"><
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-14.</p>
+    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-15.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

diff --git a/docs/about-the-author.html b/docs/about-the-author.html
@@ -131,7 +131,7 @@ <h1>About the author<a class="anchor" aria-label="anchor" href="#about-the-autho
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-14.</p>
+    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-15.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

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diff --git a/docs/covariateschapter.html b/docs/covariateschapter.html
@@ -175,7 +175,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-14.</p>
+    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-15.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

diff --git a/docs/crashcourse.html b/docs/crashcourse.html
@@ -260,7 +260,7 @@ <h3>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">sample_from_posterior</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Beta.html">rbeta</a></span><span class="op">(</span><span class="fl">1000</span>, <span class="fl">20</span>, <span class="fl">39</span><span class="op">)</span> <span class="co"># draw 1000 values from posterior survival beta(20,39)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/mean.html">mean</a></span><span class="op">(</span><span class="va">sample_from_posterior</span><span class="op">)</span> <span class="co"># compute mean with Monte Carlo integration</span></span>
-<span><span class="co">## [1] 0.3416</span></span></code></pre></div>
+<span><span class="co">## [1] 0.3407</span></span></code></pre></div>
 <p>You may check that the mean we have just calculated matches closely the expectation of a beta distribution<a class="footnote-ref" tabindex="0" data-toggle="popover" data-content='&lt;p&gt;If &lt;span class="math inline"&gt;\(X\)&lt;/span&gt; is a random variable with distribution &lt;span class="math inline"&gt;\(\text{beta}(a, b)\)&lt;/span&gt;, then &lt;span class="math inline"&gt;\(E(X) = \displaystyle{\frac{a}{a + b}}\)&lt;/span&gt;&lt;/p&gt;'><sup>10</sup></a>:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fl">20</span><span class="op">/</span><span class="op">(</span><span class="fl">20</span><span class="op">+</span><span class="fl">39</span><span class="op">)</span> <span class="co"># expectation of beta(20,39)</span></span>
@@ -269,7 +269,7 @@ <h3>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/quantile.html">quantile</a></span><span class="op">(</span><span class="va">sample_from_posterior</span>, probs <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">2.5</span><span class="op">/</span><span class="fl">100</span>, <span class="fl">97.5</span><span class="op">/</span><span class="fl">100</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">##   2.5%  97.5% </span></span>
-<span><span class="co">## 0.2261 0.4634</span></span></code></pre></div>
+<span><span class="co">## 0.2294 0.4688</span></span></code></pre></div>
 </div>
 <div id="markovmodelmcmc" class="section level3" number="1.5.2">
 <h3>
@@ -581,7 +581,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-14.</p>
+    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-15.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

diff --git a/docs/dispersal.html b/docs/dispersal.html
@@ -35113,7 +35113,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-14.</p>
+    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-15.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

diff --git a/docs/hmmcapturerecapture.html b/docs/hmmcapturerecapture.html
@@ -5345,7 +5345,7 @@ <h2>
 <span>                          nchains <span class="op">=</span> <span class="va">n.chains</span><span class="op">)</span></span>
 <span><span class="va">end_time</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">end_time</span> <span class="op">-</span> <span class="va">start_time</span></span></code></pre></div>
-<pre><code>## Time difference of 18.58 secs</code></pre>
+<pre><code>## Time difference of 19.66 secs</code></pre>
 <p>We can have a look to numerical summaries:</p>
 <div class="sourceCode" id="cb120"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/MCMCvis/man/MCMCsummary.html">MCMCsummary</a></span><span class="op">(</span><span class="va">mcmc.output</span>, round <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
@@ -6097,7 +6097,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-14.</p>
+    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-15.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

diff --git a/docs/images/infectedhousefinch.jpg b/docs/images/infectedhousefinch.jpg
diff --git a/docs/images/wolfdominance.jpg b/docs/images/wolfdominance.jpg
diff --git a/docs/index.html b/docs/index.html
@@ -107,7 +107,7 @@ <h1>Welcome<a class="anchor" aria-label="anchor" href="#welcome"><i class="fas f
 <p>This book offers a Bayesian treatment of HMMs applied to capture-recapture data. You will learn to use the R package NIMBLE (<span class="citation">de Valpine et al. (<a href="references.html#ref-deValpine2017">2017</a>)</span>) which is seen by many as the future of Bayesian statistical ecology to deal with complex models and/or big data. An important part of the book consists in case studies presented in a tutorial style to abide by the “learning by doing” philosophy.</p>
 <p>I’m currently writing this book, and I welcome any feedback. You may raise an issue <a href="https://github.com/oliviergimenez/banana-book/issues">here</a>, amend directly the R Markdown file that generated the page you’re reading by clicking on the ‘Edit this page’ icon in the right panel, or <a href="mailto:[email protected]">email me</a>. Many thanks!</p>
 <p>Olivier Gimenez. Written in Montpellier, France and Athens, Greece.
-Last updated: August 14, 2023</p>
+Last updated: August 15, 2023</p>
 <div id="license" class="section level2 unnumbered">
 <h2>License<a class="anchor" aria-label="anchor" href="#license"><i class="fas fa-link"></i></a>
 </h2>
@@ -141,7 +141,7 @@ <h2>License<a class="anchor" aria-label="anchor" href="#license"><i class="fas f
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-14.</p>
+    <p>"<strong>Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models</strong>: Theory and Case Studies in R" was written by Olivier Gimenez. It was last built on 2023-08-15.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

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+<li><a class="" href="introduction.html">Introduction</a></li>
+<li class="book-part">II. Transitions</li>
+<li><a class="active" href="introduction-1.html">Introduction</a></li>
+<li class="book-part">III. Case studies</li>
+<li><a class="" href="introduction-2.html">Introduction</a></li>
+<li><a class="" href="covariateschapter.html"><span class="header-section-number">1</span> Covariates</a></li>
+<li><a class="" href="tradeoffs.html"><span class="header-section-number">2</span> Life history</a></li>
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