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diff --git a/manual/404.html b/manual/404.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Page not found | SSMSE user manual</title>
   <meta name="description" content="This is a user manual for the SSMSE package. It includes documentation and examples." />
-  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Page not found | SSMSE user manual" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2023-08-10" />
+<meta name="date" content="2023-09-06" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/manual/M-case-study-ex.html b/manual/M-case-study-ex.html
diff --git a/manual/SSMSE.html b/manual/SSMSE.html
diff --git a/manual/advanced-options-use-a-custom-management-strategyprocedure.html b/manual/advanced-options-use-a-custom-management-strategyprocedure.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>3 Advanced options: use a custom management strategy/procedure | SSMSE user manual</title>
   <meta name="description" content="This is a user manual for the SSMSE package. It includes documentation and examples." />
-  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />
 
   <meta property="og:title" content="3 Advanced options: use a custom management strategy/procedure | SSMSE user manual" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2023-08-10" />
+<meta name="date" content="2023-09-06" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
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diff --git a/manual/glossary-of-mse-terms.html b/manual/glossary-of-mse-terms.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>9 Glossary of MSE terms | SSMSE user manual</title>
   <meta name="description" content="This is a user manual for the SSMSE package. It includes documentation and examples." />
-  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
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   <meta property="og:title" content="9 Glossary of MSE terms | SSMSE user manual" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2023-08-10" />
+<meta name="date" content="2023-09-06" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/manual/helper.html b/manual/helper.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>6 Helper functions in SSMSE | SSMSE user manual</title>
   <meta name="description" content="This is a user manual for the SSMSE package. It includes documentation and examples." />
-  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />
 
   <meta property="og:title" content="6 Helper functions in SSMSE | SSMSE user manual" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2023-08-10" />
+<meta name="date" content="2023-09-06" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/manual/index.html b/manual/index.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>SSMSE user manual</title>
   <meta name="description" content="This is a user manual for the SSMSE package. It includes documentation and examples." />
-  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />
 
   <meta property="og:title" content="SSMSE user manual" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2023-08-10" />
+<meta name="date" content="2023-09-06" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -230,7 +230,7 @@ <h1>
 <div id="header">
 <h1 class="title">SSMSE user manual</h1>
 <p class="author"><em>Kathryn Doering and Nathan Vaughan</em></p>
-<p class="date"><em>2023-08-10</em></p>
+<p class="date"><em>2023-09-06</em></p>
 </div>
 <div id="preface" class="section level1 unnumbered hasAnchor">
 <h1>Preface<a href="index.html#preface" class="anchor-section" aria-label="Anchor link to header"></a></h1>

diff --git a/manual/intro.html b/manual/intro.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>1 Introduction | SSMSE user manual</title>
   <meta name="description" content="This is a user manual for the SSMSE package. It includes documentation and examples." />
-  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />
 
   <meta property="og:title" content="1 Introduction | SSMSE user manual" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2023-08-10" />
+<meta name="date" content="2023-09-06" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/manual/output.html b/manual/output.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>7 Output and Plots | SSMSE user manual</title>
   <meta name="description" content="This is a user manual for the SSMSE package. It includes documentation and examples." />
-  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />
 
   <meta property="og:title" content="7 Output and Plots | SSMSE user manual" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2023-08-10" />
+<meta name="date" content="2023-09-06" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -232,9 +232,9 @@ <h1><span class="header-section-number">7</span> Output and Plots<a href="output
 <div id="summarizing-output" class="section level2 hasAnchor" number="7.1">
 <h2><span class="header-section-number">7.1</span> Summarizing output<a href="output.html#summarizing-output" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>Output is summarized using <code>SSMSE_summary_all()</code>:</p>
-<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb63-1"><a href="output.html#cb63-1" aria-hidden="true" tabindex="-1"></a>summary_list <span class="ot">&lt;-</span> <span class="fu">SSMSE_summary_all</span>(<span class="at">dir =</span> <span class="st">&quot;path/to/scenario/dir&quot;</span>,</span>
-<span id="cb63-2"><a href="output.html#cb63-2" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scenarios =</span> <span class="fu">c</span>(<span class="st">&quot;sample_low&quot;</span>, <span class="st">&quot;sample_high&quot;</span>),</span>
-<span id="cb63-3"><a href="output.html#cb63-3" aria-hidden="true" tabindex="-1"></a>                  <span class="at">run_parallel =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
+<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb64-1"><a href="output.html#cb64-1" aria-hidden="true" tabindex="-1"></a>summary_list <span class="ot">&lt;-</span> <span class="fu">SSMSE_summary_all</span>(<span class="at">dir =</span> <span class="st">&quot;path/to/scenario/dir&quot;</span>,</span>
+<span id="cb64-2"><a href="output.html#cb64-2" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scenarios =</span> <span class="fu">c</span>(<span class="st">&quot;sample_low&quot;</span>, <span class="st">&quot;sample_high&quot;</span>),</span>
+<span id="cb64-3"><a href="output.html#cb64-3" aria-hidden="true" tabindex="-1"></a>                  <span class="at">run_parallel =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
 <p>Relying on <code>ss3sim::get_results_all()</code>, this function creates:</p>
 <ul>
 <li>For each scenario, 3 scenario level .csv files</li>

diff --git a/manual/plotting-output-and-performance-metrics.html b/manual/plotting-output-and-performance-metrics.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>8 Plotting output and performance metrics | SSMSE user manual</title>
   <meta name="description" content="This is a user manual for the SSMSE package. It includes documentation and examples." />
-  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />
 
   <meta property="og:title" content="8 Plotting output and performance metrics | SSMSE user manual" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2023-08-10" />
+<meta name="date" content="2023-09-06" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/manual/search_index.json b/manual/search_index.json
diff --git a/manual/simple.html b/manual/simple.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>2 A simple example | SSMSE user manual</title>
   <meta name="description" content="This is a user manual for the SSMSE package. It includes documentation and examples." />
-  <meta name="generator" content="bookdown 0.34 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />
 
   <meta property="og:title" content="2 A simple example | SSMSE user manual" />
   <meta property="og:type" content="book" />
@@ -23,7 +23,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2023-08-10" />
+<meta name="date" content="2023-09-06" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -236,7 +236,7 @@ <h1><span class="header-section-number">2</span> A simple example<a href="simple
 <div id="setup-r-workspace-folders" class="section level2 hasAnchor" number="2.1">
 <h2><span class="header-section-number">2.1</span> Setup R workspace folders<a href="simple.html#setup-r-workspace-folders" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>First, we will load the <code>SSMSE</code> package and create a folder in which to run the example:</p>
-<pre><code>Installing 5 packages: mvtnorm, bdsmatrix, numDeriv, cpp11, bbmle</code></pre>
+<pre><code>Installing 4 packages: mvtnorm, bdsmatrix, numDeriv, bbmle</code></pre>
 <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="simple.html#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(SSMSE) <span class="co">#load the package</span></span>
 <span id="cb4-2"><a href="simple.html#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(r4ss) <span class="co">#install using remotes::install_github(&quot;r4ss/r4ss)</span></span>
 <span id="cb4-3"><a href="simple.html#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(foreach) <span class="co">#if using run_parallel = TRUE</span></span>