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Quarto GHA Workflow Runner committed Apr 26, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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61 changes: 45 additions & 16 deletions content/AFSC-BSAI-AtkaMackerel.html
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Expand Up @@ -2,7 +2,7 @@
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.550">
<meta name="generator" content="quarto-1.4.553">

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

Expand Down Expand Up @@ -194,6 +194,12 @@
<a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">SWFSC sardine case study</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../content/NWFSC-petrale.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">NWFSC petrale case study</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
Expand Down Expand Up @@ -246,7 +252,7 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Names of required packages</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>packages <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="st">"dplyr"</span>, <span class="st">"tidyr"</span>, <span class="st">"ggplot2"</span>, <span class="st">"TMB"</span>, <span class="st">"reshape2"</span>, <span class="st">"here"</span>, <span class="st">"remotes"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>packages <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="st">"dplyr"</span>, <span class="st">"tidyr"</span>, <span class="st">"ggplot2"</span>, <span class="st">"TMB"</span>, <span class="st">"reshape2"</span>, <span class="st">"here"</span>, <span class="st">"remotes"</span>, <span class="st">"lubridate"</span>)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co"># Install packages not yet installed</span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>installed_packages <span class="ot">&lt;-</span> packages <span class="sc">%in%</span> <span class="fu">rownames</span>(<span class="fu">installed.packages</span>())</span>
Expand All @@ -256,16 +262,17 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a>remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"kaskr/TMB_contrib_R/TMBhelper"</span>)</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a>remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"NOAA-FIMS/FIMS"</span>)</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="co"># Load packages</span></span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="fu">invisible</span>(<span class="fu">lapply</span>(packages, library, <span class="at">character.only =</span> <span class="cn">TRUE</span>))</span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(FIMS)</span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(TMBhelper)</span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a>R_version <span class="ot">&lt;-</span> version<span class="sc">$</span>version.string</span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a>TMB_version <span class="ot">&lt;-</span> <span class="fu">packageDescription</span>(<span class="st">"TMB"</span>)<span class="sc">$</span>Version</span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a>FIMS_commit <span class="ot">&lt;-</span> <span class="fu">substr</span>(<span class="fu">packageDescription</span>(<span class="st">"FIMS"</span>)<span class="sc">$</span>GithubSHA1, <span class="dv">1</span>, <span class="dv">7</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a>remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"r4ss/r4ss"</span>)</span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="co"># Load packages</span></span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="fu">invisible</span>(<span class="fu">lapply</span>(packages, library, <span class="at">character.only =</span> <span class="cn">TRUE</span>))</span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(FIMS)</span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(TMBhelper)</span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a>R_version <span class="ot">&lt;-</span> version<span class="sc">$</span>version.string</span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a>TMB_version <span class="ot">&lt;-</span> <span class="fu">packageDescription</span>(<span class="st">"TMB"</span>)<span class="sc">$</span>Version</span>
<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a>FIMS_commit <span class="ot">&lt;-</span> <span class="fu">substr</span>(<span class="fu">packageDescription</span>(<span class="st">"FIMS"</span>)<span class="sc">$</span>GithubSHA1, <span class="dv">1</span>, <span class="dv">7</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<div class="cell">
Expand All @@ -280,11 +287,11 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
</details>
</div>
<ul>
<li>R version: R version 4.3.2 (2023-10-31)<br>
<li>R version: R version 4.4.0 (2024-04-24)<br>
</li>
<li>TMB version: 1.9.10<br>
<li>TMB version: 1.9.11<br>
</li>
<li>FIMS commit: 18f96a8<br>
<li>FIMS commit: 97281c2<br>
</li>
<li>Stock name: BSAI Atka mackerel<br>
</li>
Expand Down Expand Up @@ -656,6 +663,24 @@ <h2 class="anchored" data-anchor-id="script-that-sets-up-and-runs-the-model">Scr
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp("https:\/\/noaa-fims\.github\.io\/case-studies");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
Expand Down Expand Up @@ -690,7 +715,11 @@ <h2 class="anchored" data-anchor-id="script-that-sets-up-and-runs-the-model">Scr
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
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