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Quarto GHA Workflow Runner committed Jan 22, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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425 changes: 223 additions & 202 deletions DAISIE.html
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129 changes: 71 additions & 58 deletions DAISIEprep.html
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578 changes: 578 additions & 0 deletions assignment.html
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201 changes: 47 additions & 154 deletions insula_tutorial_intro.html → exercise.html
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44 changes: 30 additions & 14 deletions index.html
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<meta name="author" content="Luis Valente, Joshua W. Lambert">

<title>LearnDAISIEprep</title>
<title>Island Biology DAISIE Practical</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
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<script src="site_libs/quarto-search/fuse.min.js"></script>
<script src="site_libs/quarto-search/quarto-search.js"></script>
<meta name="quarto:offset" content="./">
<link href="./install_packages.html" rel="next">
<link href="./installation.html" rel="next">
<script src="site_libs/quarto-html/quarto.js"></script>
<script src="site_libs/quarto-html/popper.min.js"></script>
<script src="site_libs/quarto-html/tippy.umd.min.js"></script>
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}</script>


<link rel="stylesheet" href="styles.css">
</head>

<body class="nav-sidebar floating">
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<nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
<div class="pt-lg-2 mt-2 text-left sidebar-header">
<div class="sidebar-title mb-0 py-0">
<a href="./">LearnDAISIEprep</a>
<a href="./">Island Biology DAISIE Practical</a>
<div class="sidebar-tools-main">
<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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</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./install_packages.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Install packages</span></span></a>
<a href="./installation.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Installation</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./insula_tutorial_intro.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Insula practical tutorial</span></span></a>
<a href="./introduction.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Introduction</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./assignment.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Assignment Instructions</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./DAISIEprep.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">DAISIEprep</span></span></a>
<span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">DAISIEprep</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./DAISIE.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">DAISIE</span></span></a>
<span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">DAISIE</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./exercise.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Insula beetles exercise</span></span></a>
</div>
</li>
</ul>
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<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">LearnDAISIEprep</h1>
<h1 class="title">Island Biology DAISIE Practical</h1>
</div>


Expand All @@ -169,7 +180,12 @@ <h1 class="title">LearnDAISIEprep</h1>

</header>

<p>Welcome to the LearnDAISIEprep website. Here you will find material to learn how to use the DAISIE ecosystem of R package to analyse the ecology and evolution of island communities. These tools have been developed to answer research questions in island biogeography and macroevolutionary science and can be powerful tools when applied appropriately.</p>
<p>Welcome to the DAISIE computer practical of the Island Biology course. Here you will find the material to learn how to use the DAISIE ecosystem of R packages to analyse the ecology and evolution of island communities. These tools have been developed to answer research questions in island biogeography and macroevolution. We will apply them to a case study of a group of beetles from the Caribbean islands.</p>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="images/Figure_Insula_ancestral_state_reconstruction.png" class="img-fluid figure-img" width="400"></p>
</figure>
</div>



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<div class="nav-page nav-page-previous">
</div>
<div class="nav-page nav-page-next">
<a href="./install_packages.html" class="pagination-link">
<span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Install packages</span></span> <i class="bi bi-arrow-right-short"></i>
<a href="./installation.html" class="pagination-link">
<span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Installation</span></span> <i class="bi bi-arrow-right-short"></i>
</a>
</div>
</nav>
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65 changes: 40 additions & 25 deletions install_packages.html → installation.html
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<meta name="author" content="Luis Valente">

<title>LearnDAISIEprep - 2&nbsp; Install packages</title>
<title>Island Biology DAISIE Practical - 2&nbsp; Installation</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
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<script src="site_libs/quarto-search/fuse.min.js"></script>
<script src="site_libs/quarto-search/quarto-search.js"></script>
<meta name="quarto:offset" content="./">
<link href="./insula_tutorial_intro.html" rel="next">
<link href="./introduction.html" rel="next">
<link href="./index.html" rel="prev">
<script src="site_libs/quarto-html/quarto.js"></script>
<script src="site_libs/quarto-html/popper.min.js"></script>
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}</script>


<link rel="stylesheet" href="styles.css">
</head>

<body class="nav-sidebar floating">
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<button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<i class="bi bi-layout-text-sidebar-reverse"></i>
</button>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./install_packages.html"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Install packages</span></a></li></ol></nav>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./installation.html"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Installation</span></a></li></ol></nav>
<a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
</a>
<button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
Expand All @@ -127,7 +126,7 @@
<nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
<div class="pt-lg-2 mt-2 text-left sidebar-header">
<div class="sidebar-title mb-0 py-0">
<a href="./">LearnDAISIEprep</a>
<a href="./">Island Biology DAISIE Practical</a>
<div class="sidebar-tools-main">
<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>
Expand All @@ -148,26 +147,38 @@
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./install_packages.html" class="sidebar-item-text sidebar-link active">
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Install packages</span></span></a>
<a href="./installation.html" class="sidebar-item-text sidebar-link active">
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Installation</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./insula_tutorial_intro.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Insula practical tutorial</span></span></a>
<a href="./introduction.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Introduction</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./assignment.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Assignment Instructions</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./DAISIEprep.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">DAISIEprep</span></span></a>
<span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">DAISIEprep</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./DAISIE.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">DAISIE</span></span></a>
<span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">DAISIE</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./exercise.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Insula beetles exercise</span></span></a>
</div>
</li>
</ul>
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<h2 id="toc-title">Table of contents</h2>

<ul>
<li><a href="#open-and-run-this-script-in-rstudio" id="toc-open-and-run-this-script-in-rstudio" class="nav-link active" data-scroll-target="#open-and-run-this-script-in-rstudio"><span class="header-section-number">2.1</span> Open and run this script in Rstudio</a>
<ul class="collapse">
<li><a href="#install-required-packages" id="toc-install-required-packages" class="nav-link" data-scroll-target="#install-required-packages"><span class="header-section-number">2.1.1</span> Install required packages</a></li>
</ul></li>
<li><a href="#install-required-software" id="toc-install-required-software" class="nav-link active" data-scroll-target="#install-required-software"><span class="header-section-number">2.1</span> Install required software:</a></li>
<li><a href="#install-required-r-packages" id="toc-install-required-r-packages" class="nav-link" data-scroll-target="#install-required-r-packages"><span class="header-section-number">2.2</span> Install required R packages</a></li>
</ul>
</nav>
</div>
Expand All @@ -192,7 +201,7 @@ <h2 id="toc-title">Table of contents</h2>

<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Install packages</span></h1>
<h1 class="title"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Installation</span></h1>
</div>


Expand All @@ -213,14 +222,21 @@ <h1 class="title"><span class="chapter-number">2</span>&nbsp; <span class="chapt

</header>

<section id="open-and-run-this-script-in-rstudio" class="level2" data-number="2.1">
<h2 data-number="2.1" class="anchored" data-anchor-id="open-and-run-this-script-in-rstudio"><span class="header-section-number">2.1</span> Open and run this script in Rstudio</h2>
<section id="install-required-packages" class="level3" data-number="2.1.1">
<h3 data-number="2.1.1" class="anchored" data-anchor-id="install-required-packages"><span class="header-section-number">2.1.1</span> Install required packages</h3>
<section id="install-required-software" class="level2" data-number="2.1">
<h2 data-number="2.1" class="anchored" data-anchor-id="install-required-software"><span class="header-section-number">2.1</span> Install required software:</h2>
<ul>
<li><p><a href="https://www.r-project.org">R</a></p></li>
<li><p><a href="https://posit.co">Rstudio</a></p></li>
<li><p><a href="https://github.com/rambaut/figtree/releases">Figtree</a></p></li>
</ul>
</section>
<section id="install-required-r-packages" class="level2" data-number="2.2">
<h2 data-number="2.2" class="anchored" data-anchor-id="install-required-r-packages"><span class="header-section-number">2.2</span> Install required R packages</h2>
<p>Open and run this script in Rstudio. This should install all required R packages (<strong>may take a while!</strong>).</p>
<div class="cell">
<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="fu">install.packages</span>(<span class="st">'DAISIE'</span>,<span class="at">dependencies =</span> <span class="cn">TRUE</span>)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">'ape'</span>,<span class="at">dependencies =</span> <span class="cn">TRUE</span>)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">'DAISIEprep'</span>,<span class="at">dependencies =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">'DAISIEprep'</span>,<span class="at">dependencies =</span> <span class="cn">TRUE</span>)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">'ape'</span>,<span class="at">dependencies =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Check if packages load correctly</p>
<div class="cell">
Expand All @@ -230,7 +246,6 @@ <h3 data-number="2.1.1" class="anchored" data-anchor-id="install-required-packag
</div>


</section>
</section>

</main> <!-- /main -->
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</a>
</div>
<div class="nav-page nav-page-next">
<a href="./insula_tutorial_intro.html" class="pagination-link">
<span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Insula practical tutorial</span></span> <i class="bi bi-arrow-right-short"></i>
<a href="./introduction.html" class="pagination-link">
<span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Introduction</span></span> <i class="bi bi-arrow-right-short"></i>
</a>
</div>
</nav>
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