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k-doering-NOAA committed Aug 10, 2023
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2 changes: 1 addition & 1 deletion manual/404.html
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<meta name="author" content="Kathryn Doering and Nathan Vaughan" />


<meta name="date" content="2023-08-09" />
<meta name="date" content="2023-08-10" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
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2 changes: 1 addition & 1 deletion manual/M-case-study-ex.html
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2 changes: 1 addition & 1 deletion manual/SSMSE.html
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2 changes: 1 addition & 1 deletion manual/advanced-options-use-a-custom-management-strategyprocedure.html
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2 changes: 1 addition & 1 deletion manual/glossary-of-mse-terms.html
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2 changes: 1 addition & 1 deletion manual/helper.html
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<meta name="date" content="2023-08-09" />
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6 changes: 3 additions & 3 deletions manual/index.html
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<meta name="author" content="Kathryn Doering and Nathan Vaughan" />


<meta name="date" content="2023-08-09" />
<meta name="date" content="2023-08-10" />

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<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>2023-08-09</em></p>
<p class="date"><em>2023-08-10</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>
Expand All @@ -244,7 +244,7 @@ <h2>R session information<a href="index.html#r-session-information" class="ancho
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="index.html#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span></code></pre></div>
<pre><code>R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Running under: Ubuntu 22.04.3 LTS

Matrix products: default

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2 changes: 1 addition & 1 deletion manual/intro.html
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2 changes: 1 addition & 1 deletion manual/output.html
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2 changes: 1 addition & 1 deletion manual/plotting-output-and-performance-metrics.html
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2 changes: 1 addition & 1 deletion manual/search_index.json
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4 changes: 2 additions & 2 deletions manual/simple.html
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<meta name="date" content="2023-08-09" />
<meta name="date" content="2023-08-10" />

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Expand Down Expand Up @@ -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 4 packages: mvtnorm, bdsmatrix, numDeriv, bbmle</code></pre>
<pre><code>Installing 5 packages: mvtnorm, bdsmatrix, numDeriv, cpp11, 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>
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