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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Installation · PhyloDiamond.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../index.html"><img src="../assets/logo.png" alt="PhyloDiamond.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="../index.html">PhyloDiamond.jl</a></span></div><form class="docs-search" action="../search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../index.html">Home</a></li><li><span class="tocitem">Manual</span><ul><li class="is-active"><a class="tocitem" href="installation.html">Installation</a><ul class="internal"><li><a class="tocitem" href="#Installation-of-Julia"><span>Installation of Julia</span></a></li><li><a class="tocitem" href="#Installation-of-the-PhyloDiamond.jl-package"><span>Installation of the <code>PhyloDiamond.jl</code> package</span></a></li><li><a class="tocitem" href="#Loading-the-Package"><span>Loading the Package</span></a></li></ul></li><li><a class="tocitem" href="implementation.html">Implementation</a></li></ul></li><li><span class="tocitem">Library</span><ul><li><a class="tocitem" href="../lib/public_methods.html">Public Methods</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Manual</a></li><li class="is-active"><a href="installation.html">Installation</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="installation.html">Installation</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/solislemuslab/phylo-invariants/blob/master/docs/src/man/installation.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h1><h2 id="Installation-of-Julia"><a class="docs-heading-anchor" href="#Installation-of-Julia">Installation of Julia</a><a id="Installation-of-Julia-1"></a><a class="docs-heading-anchor-permalink" href="#Installation-of-Julia" title="Permalink"></a></h2><p>Julia is a high-level and interactive programming language (like R or Matlab), but it is also high-performance (like C). To install Julia, follow instructions <a href="http://julialang.org/downloads/">here</a>. For a quick &amp; basic tutorial on Julia, see <a href="http://learnxinyminutes.com/docs/julia/">learn x in y minutes</a>.</p><p>Text editors:</p><ul><li><a href="https://code.visualstudio.com">Visual Studio Code</a> provides an editor and an integrated development environment (IDE) for Julia: highly recommended!</li><li>You can also run Julia within a <a href="http://jupyter.org">Jupyter</a> notebook (formerly IPython notebook).</li></ul><p>IMPORTANT: Julia code is just-in-time compiled. This means that the first time you run a function, it will be compiled at that moment. So, please be patient! Future calls to the function will be much much faster. Trying out toy examples for the first calls is a good idea.</p><h2 id="Installation-of-the-PhyloDiamond.jl-package"><a class="docs-heading-anchor" href="#Installation-of-the-PhyloDiamond.jl-package">Installation of the <code>PhyloDiamond.jl</code> package</a><a id="Installation-of-the-PhyloDiamond.jl-package-1"></a><a class="docs-heading-anchor-permalink" href="#Installation-of-the-PhyloDiamond.jl-package" title="Permalink"></a></h2><p>To install the package, type inside Julia:</p><pre><code class="language-julia hljs">]
add PhyloDiamond</code></pre><p>Installation can take a few minutes, please be patient.</p><p>The <code>PhyloDiamond.jl</code> package has dependencies like <a href="https://juliastats.org/Distributions.jl/stable/starting/">Distributions</a> and <a href="http://juliadata.github.io/DataFrames.jl/stable/">DataFrames</a> (see the <code>Project.toml</code> file for the full list), but everything is installed automatically.</p><h2 id="Loading-the-Package"><a class="docs-heading-anchor" href="#Loading-the-Package">Loading the Package</a><a id="Loading-the-Package-1"></a><a class="docs-heading-anchor-permalink" href="#Loading-the-Package" title="Permalink"></a></h2><p>To check that your installation worked, type this in Julia to load the package. This is something to type every time you start a Julia session:</p><pre><code class="language-julia hljs">using PhyloDiamond</code></pre><p>This step can also take a while, if Julia needs to pre-compile the code (after a package update for instance).</p><p>Press <code>?</code> inside Julia to switch to help mode,  followed by the name of a function (or type) to get more details about it.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../index.html">« Home</a><a class="docs-footer-nextpage" href="implementation.html">Implementation »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Monday 13 March 2023 21:25">Monday 13 March 2023</span>. Using Julia version 1.8.0-rc1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
