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Quarto GHA Workflow Runner committed Oct 18, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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8 changes: 4 additions & 4 deletions content/AFSC-BSAI-AtkaMackerel.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.55">
<meta name="generator" content="quarto-1.5.57">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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</a>
<div class="sidebar-tools-main tools-wide">
<a href="https://nmfs-opensci.github.io" title="NMFS Open Science" class="quarto-navigation-tool px-1" aria-label="NMFS Open Science"><i class="bi bi-globe"></i></a>
<a href="https://github.com/nmfs-opensci" title="NMFS OpenSci" class="quarto-navigation-tool px-1" aria-label="NMFS OpenSci"><i class="bi bi-github"></i></a>
<a href="https://github.com/NOAA-FIMS/case-studies" title="NOAA FIMS case studies" class="quarto-navigation-tool px-1" aria-label="NOAA FIMS case studies"><i class="bi bi-github"></i></a>
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</div>
</div>
Expand Down Expand Up @@ -301,9 +301,9 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
<ul>
<li>R version: R version 4.4.1 (2024-06-14)<br>
</li>
<li>TMB version: 1.9.14<br>
<li>TMB version: 1.9.15<br>
</li>
<li>FIMS commit: 081972c<br>
<li>FIMS commit: f0d4e76<br>
</li>
<li>Stock name: BSAI Atka mackerel<br>
</li>
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491 changes: 245 additions & 246 deletions content/AFSC-GOA-pollock.html
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8 changes: 4 additions & 4 deletions content/NEFSC-yellowtail.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.55">
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</a>
<div class="sidebar-tools-main tools-wide">
<a href="https://nmfs-opensci.github.io" title="NMFS Open Science" class="quarto-navigation-tool px-1" aria-label="NMFS Open Science"><i class="bi bi-globe"></i></a>
<a href="https://github.com/nmfs-opensci" title="NMFS OpenSci" class="quarto-navigation-tool px-1" aria-label="NMFS OpenSci"><i class="bi bi-github"></i></a>
<a href="https://github.com/NOAA-FIMS/case-studies" title="NOAA FIMS case studies" class="quarto-navigation-tool px-1" aria-label="NOAA FIMS case studies"><i class="bi bi-github"></i></a>
<a href="" class="quarto-color-scheme-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleColorScheme(); return false;" title="Toggle dark mode"><i class="bi"></i></a>
</div>
</div>
Expand Down Expand Up @@ -302,9 +302,9 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
<ul>
<li>R version: R version 4.4.1 (2024-06-14)<br>
</li>
<li>TMB version: 1.9.14<br>
<li>TMB version: 1.9.15<br>
</li>
<li>FIMS commit: 081972c<br>
<li>FIMS commit: f0d4e76<br>
</li>
<li>Stock name: Southern New England-Mid Atlantic Yellowtail Flounder<br>
</li>
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12 changes: 6 additions & 6 deletions content/NWFSC-petrale.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.55">
<meta name="generator" content="quarto-1.5.57">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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</a>
<div class="sidebar-tools-main tools-wide">
<a href="https://nmfs-opensci.github.io" title="NMFS Open Science" class="quarto-navigation-tool px-1" aria-label="NMFS Open Science"><i class="bi bi-globe"></i></a>
<a href="https://github.com/nmfs-opensci" title="NMFS OpenSci" class="quarto-navigation-tool px-1" aria-label="NMFS OpenSci"><i class="bi bi-github"></i></a>
<a href="https://github.com/NOAA-FIMS/case-studies" title="NOAA FIMS case studies" class="quarto-navigation-tool px-1" aria-label="NOAA FIMS case studies"><i class="bi bi-github"></i></a>
<a href="" class="quarto-color-scheme-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleColorScheme(); return false;" title="Toggle dark mode"><i class="bi"></i></a>
</div>
</div>
Expand Down Expand Up @@ -303,9 +303,9 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
<ul>
<li>R version: R version 4.4.1 (2024-06-14)<br>
</li>
<li>TMB version: 1.9.14<br>
<li>TMB version: 1.9.15<br>
</li>
<li>FIMS commit: 081972c<br>
<li>FIMS commit: f0d4e76<br>
</li>
<li>Stock name: West Coast Petrale Sole<br>
</li>
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<span id="cb3-27"><a href="#cb3-27" aria-hidden="true" tabindex="-1"></a><span class="co"># by assigning to fleet -1, these get filtered by get_ss3_data()</span></span>
<span id="cb3-28"><a href="#cb3-28" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-29"><a href="#cb3-29" aria-hidden="true" tabindex="-1"></a><span class="co"># only include age comps with fleet = -4 or 1:</span></span>
<span id="cb3-30"><a href="#cb3-30" aria-hidden="true" tabindex="-1"></a>ss3dat<span class="sc">$</span>agecomp <span class="ot">&lt;-</span> ss3dat<span class="sc">$</span>agecomp <span class="sc">|&gt;</span> dplyr<span class="sc">::</span><span class="fu">filter</span>(FltSvy <span class="sc">%in%</span> <span class="fu">c</span>(<span class="sc">-</span><span class="dv">4</span>, <span class="dv">1</span>))</span>
<span id="cb3-31"><a href="#cb3-31" aria-hidden="true" tabindex="-1"></a>ss3dat<span class="sc">$</span>agecomp<span class="sc">$</span>FltSvy <span class="ot">&lt;-</span> <span class="fu">abs</span>(ss3dat<span class="sc">$</span>agecomp<span class="sc">$</span>FltSvy)</span>
<span id="cb3-30"><a href="#cb3-30" aria-hidden="true" tabindex="-1"></a>ss3dat<span class="sc">$</span>agecomp <span class="ot">&lt;-</span> ss3dat<span class="sc">$</span>agecomp <span class="sc">|&gt;</span> dplyr<span class="sc">::</span><span class="fu">filter</span>(fleet <span class="sc">%in%</span> <span class="fu">c</span>(<span class="sc">-</span><span class="dv">4</span>, <span class="dv">1</span>))</span>
<span id="cb3-31"><a href="#cb3-31" aria-hidden="true" tabindex="-1"></a>ss3dat<span class="sc">$</span>agecomp<span class="sc">$</span>fleet <span class="ot">&lt;-</span> <span class="fu">abs</span>(ss3dat<span class="sc">$</span>agecomp<span class="sc">$</span>fleet)</span>
<span id="cb3-32"><a href="#cb3-32" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-33"><a href="#cb3-33" aria-hidden="true" tabindex="-1"></a><span class="co"># convert SS3 data into FIMS format using function defined in the R directory</span></span>
<span id="cb3-34"><a href="#cb3-34" aria-hidden="true" tabindex="-1"></a>mydat <span class="ot">&lt;-</span> <span class="fu">get_ss3_data</span>(ss3dat, <span class="at">fleets =</span> <span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">4</span>), <span class="at">ages =</span> ages)</span>
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4 changes: 2 additions & 2 deletions content/PIFS-opakapaka.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.55">
<meta name="generator" content="quarto-1.5.57">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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</a>
<div class="sidebar-tools-main tools-wide">
<a href="https://nmfs-opensci.github.io" title="NMFS Open Science" class="quarto-navigation-tool px-1" aria-label="NMFS Open Science"><i class="bi bi-globe"></i></a>
<a href="https://github.com/nmfs-opensci" title="NMFS OpenSci" class="quarto-navigation-tool px-1" aria-label="NMFS OpenSci"><i class="bi bi-github"></i></a>
<a href="https://github.com/NOAA-FIMS/case-studies" title="NOAA FIMS case studies" class="quarto-navigation-tool px-1" aria-label="NOAA FIMS case studies"><i class="bi bi-github"></i></a>
<a href="" class="quarto-color-scheme-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleColorScheme(); return false;" title="Toggle dark mode"><i class="bi"></i></a>
</div>
</div>
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8 changes: 4 additions & 4 deletions content/SEFSC-scamp.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.55">
<meta name="generator" content="quarto-1.5.57">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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</a>
<div class="sidebar-tools-main tools-wide">
<a href="https://nmfs-opensci.github.io" title="NMFS Open Science" class="quarto-navigation-tool px-1" aria-label="NMFS Open Science"><i class="bi bi-globe"></i></a>
<a href="https://github.com/nmfs-opensci" title="NMFS OpenSci" class="quarto-navigation-tool px-1" aria-label="NMFS OpenSci"><i class="bi bi-github"></i></a>
<a href="https://github.com/NOAA-FIMS/case-studies" title="NOAA FIMS case studies" class="quarto-navigation-tool px-1" aria-label="NOAA FIMS case studies"><i class="bi bi-github"></i></a>
<a href="" class="quarto-color-scheme-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleColorScheme(); return false;" title="Toggle dark mode"><i class="bi"></i></a>
</div>
</div>
Expand Down Expand Up @@ -300,9 +300,9 @@ <h2 class="anchored" data-anchor-id="setup-description">Setup description</h2>
<ul>
<li>R version: R version 4.4.1 (2024-06-14)<br>
</li>
<li>TMB version: 1.9.14<br>
<li>TMB version: 1.9.15<br>
</li>
<li>FIMS commit: 081972c<br>
<li>FIMS commit: f0d4e76<br>
</li>
<li>Stock name: South Atlantic scamp grouper<br>
</li>
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12 changes: 6 additions & 6 deletions content/SWFSC-sardine.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.55">
<meta name="generator" content="quarto-1.5.57">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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</a>
<div class="sidebar-tools-main tools-wide">
<a href="https://nmfs-opensci.github.io" title="NMFS Open Science" class="quarto-navigation-tool px-1" aria-label="NMFS Open Science"><i class="bi bi-globe"></i></a>
<a href="https://github.com/nmfs-opensci" title="NMFS OpenSci" class="quarto-navigation-tool px-1" aria-label="NMFS OpenSci"><i class="bi bi-github"></i></a>
<a href="https://github.com/NOAA-FIMS/case-studies" title="NOAA FIMS case studies" class="quarto-navigation-tool px-1" aria-label="NOAA FIMS case studies"><i class="bi bi-github"></i></a>
<a href="" class="quarto-color-scheme-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleColorScheme(); return false;" title="Toggle dark mode"><i class="bi"></i></a>
</div>
</div>
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<ul>
<li>R version: R version 4.4.1 (2024-06-14)<br>
</li>
<li>TMB version: 1.9.14<br>
<li>TMB version: 1.9.15<br>
</li>
<li>FIMS commit: 081972c<br>
<li>FIMS commit: f0d4e76<br>
</li>
<li>Stock name: Pacific sardine northern subpopulation<br>
</li>
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<span id="cb5-251"><a href="#cb5-251" aria-hidden="true" tabindex="-1"></a>ewaa_growth<span class="sc">$</span>ages <span class="ot">&lt;-</span> ages</span>
<span id="cb5-252"><a href="#cb5-252" aria-hidden="true" tabindex="-1"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: getting weight-at-age vector from</span></span>
<span id="cb5-253"><a href="#cb5-253" aria-hidden="true" tabindex="-1"></a><span class="co"># petrale_output$wtatage |&gt;</span></span>
<span id="cb5-254"><a href="#cb5-254" aria-hidden="true" tabindex="-1"></a><span class="co"># dplyr::filter(Sex == 1 &amp; Fleet == -1 &amp; Yr == 1876) |&gt;</span></span>
<span id="cb5-254"><a href="#cb5-254" aria-hidden="true" tabindex="-1"></a><span class="co"># dplyr::filter(sex == 1 &amp; fleet == -1 &amp; year == 1876) |&gt;</span></span>
<span id="cb5-255"><a href="#cb5-255" aria-hidden="true" tabindex="-1"></a><span class="co"># dplyr::select(paste(0:40)) |&gt;</span></span>
<span id="cb5-256"><a href="#cb5-256" aria-hidden="true" tabindex="-1"></a><span class="co"># round(4)</span></span>
<span id="cb5-257"><a href="#cb5-257" aria-hidden="true" tabindex="-1"></a><span class="co"># ewaa_growth$weights &lt;- c(0.019490,0.077760,0.108865,</span></span>
<span id="cb5-258"><a href="#cb5-258" aria-hidden="true" tabindex="-1"></a><span class="co"># 0.133855,0.154360,0.174905,0.184200,</span></span>
<span id="cb5-259"><a href="#cb5-259" aria-hidden="true" tabindex="-1"></a><span class="co"># 0.196460,0.214155)</span></span>
<span id="cb5-260"><a href="#cb5-260" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-261"><a href="#cb5-261" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-262"><a href="#cb5-262" aria-hidden="true" tabindex="-1"></a>ewaa_growth<span class="sc">$</span>weights <span class="ot">&lt;-</span> wtatage <span class="sc">%&gt;%</span> <span class="fu">filter</span>(Fleet <span class="sc">==</span> <span class="dv">1</span>, Yr <span class="sc">==</span> <span class="dv">2010</span>) <span class="sc">%&gt;%</span> <span class="fu">select</span>(<span class="fu">as.character</span>(<span class="dv">0</span><span class="sc">:</span><span class="dv">10</span>)) <span class="sc">%&gt;%</span> t <span class="sc">%&gt;%</span></span>
<span id="cb5-262"><a href="#cb5-262" aria-hidden="true" tabindex="-1"></a>ewaa_growth<span class="sc">$</span>weights <span class="ot">&lt;-</span> wtatage <span class="sc">%&gt;%</span> <span class="fu">filter</span>(fleet <span class="sc">==</span> <span class="dv">1</span>, year <span class="sc">==</span> <span class="dv">2010</span>) <span class="sc">%&gt;%</span> <span class="fu">select</span>(<span class="fu">as.character</span>(<span class="dv">0</span><span class="sc">:</span><span class="dv">10</span>)) <span class="sc">%&gt;%</span> t <span class="sc">%&gt;%</span></span>
<span id="cb5-263"><a href="#cb5-263" aria-hidden="true" tabindex="-1"></a> as.vector</span>
<span id="cb5-264"><a href="#cb5-264" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-265"><a href="#cb5-265" aria-hidden="true" tabindex="-1"></a><span class="co"># maturity</span></span>
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.55">
<meta name="generator" content="quarto-1.5.57">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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</a>
<div class="sidebar-tools-main tools-wide">
<a href="https://nmfs-opensci.github.io" title="NMFS Open Science" class="quarto-navigation-tool px-1" aria-label="NMFS Open Science"><i class="bi bi-globe"></i></a>
<a href="https://github.com/nmfs-opensci" title="NMFS OpenSci" class="quarto-navigation-tool px-1" aria-label="NMFS OpenSci"><i class="bi bi-github"></i></a>
<a href="https://github.com/NOAA-FIMS/case-studies" title="NOAA FIMS case studies" class="quarto-navigation-tool px-1" aria-label="NOAA FIMS case studies"><i class="bi bi-github"></i></a>
<a href="" class="quarto-color-scheme-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleColorScheme(); return false;" title="Toggle dark mode"><i class="bi"></i></a>
</div>
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.55">
<meta name="generator" content="quarto-1.5.57">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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</a>
<div class="sidebar-tools-main tools-wide">
<a href="https://nmfs-opensci.github.io" title="NMFS Open Science" class="quarto-navigation-tool px-1" aria-label="NMFS Open Science"><i class="bi bi-globe"></i></a>
<a href="https://github.com/nmfs-opensci" title="NMFS OpenSci" class="quarto-navigation-tool px-1" aria-label="NMFS OpenSci"><i class="bi bi-github"></i></a>
<a href="https://github.com/NOAA-FIMS/case-studies" title="NOAA FIMS case studies" class="quarto-navigation-tool px-1" aria-label="NOAA FIMS case studies"><i class="bi bi-github"></i></a>
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4 changes: 2 additions & 2 deletions content/publishing.html
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4 changes: 2 additions & 2 deletions content/rendering.html
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