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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>AMR Plots with ggplot2 — ggplot_sir • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="AMR Plots with ggplot2 — ggplot_sir"><meta name="description" content="Use these functions to create bar plots for AMR data analysis. All functions rely on ggplot2 functions."><meta property="og:description" content="Use these functions to create bar plots for AMR data analysis. All functions rely on ggplot2 functions."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>AMR Plots with ggplot2 — ggplot_sir • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="AMR Plots with ggplot2 — ggplot_sir"><meta name="description" content="Use these functions to create bar plots for AMR data analysis. All functions rely on ggplot2 functions."><meta property="og:description" content="Use these functions to create bar plots for AMR data analysis. All functions rely on ggplot2 functions."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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@@ -55,18 +55,42 @@
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ggplot_sir</span><span class="op">(</span><span class="va">data</span>, position <span class="op">=</span> <span class="cn">NULL</span>, x <span class="op">=</span> <span class="st">"antibiotic"</span>,</span>
<span> fill <span class="op">=</span> <span class="st">"interpretation"</span>, facet <span class="op">=</span> <span class="cn">NULL</span>, breaks <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">0.1</span><span class="op">)</span>,</span>
<span> limits <span class="op">=</span> <span class="cn">NULL</span>, translate_ab <span class="op">=</span> <span class="st">"name"</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> minimum <span class="op">=</span> <span class="fl">30</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="cn">NULL</span>, colours <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S</span>
<span> <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, SI <span class="op">=</span> <span class="st">"#3CAEA3"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, IR <span class="op">=</span> <span class="st">"#ED553B"</span>,</span>
<span> R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, datalabels <span class="op">=</span> <span class="cn">TRUE</span>, datalabels.size <span class="op">=</span> <span class="fl">2.5</span>,</span>
<span> datalabels.colour <span class="op">=</span> <span class="st">"grey15"</span>, title <span class="op">=</span> <span class="cn">NULL</span>, subtitle <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> caption <span class="op">=</span> <span class="cn">NULL</span>, x.title <span class="op">=</span> <span class="st">"Antimicrobial"</span>, y.title <span class="op">=</span> <span class="st">"Proportion"</span>, <span class="va">...</span><span class="op">)</span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ggplot_sir</span><span class="op">(</span></span>
<span> <span class="va">data</span>,</span>
<span> position <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> x <span class="op">=</span> <span class="st">"antibiotic"</span>,</span>
<span> fill <span class="op">=</span> <span class="st">"interpretation"</span>,</span>
<span> facet <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> breaks <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">0.1</span><span class="op">)</span>,</span>
<span> limits <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> translate_ab <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> minimum <span class="op">=</span> <span class="fl">30</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> nrow <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> colours <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, SI <span class="op">=</span> <span class="st">"#3CAEA3"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, IR <span class="op">=</span></span>
<span> <span class="st">"#ED553B"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> datalabels <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> datalabels.size <span class="op">=</span> <span class="fl">2.5</span>,</span>
<span> datalabels.colour <span class="op">=</span> <span class="st">"grey15"</span>,</span>
<span> title <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> subtitle <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> caption <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> x.title <span class="op">=</span> <span class="st">"Antimicrobial"</span>,</span>
<span> y.title <span class="op">=</span> <span class="st">"Proportion"</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">geom_sir</span><span class="op">(</span>position <span class="op">=</span> <span class="cn">NULL</span>, x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"antibiotic"</span>, <span class="st">"interpretation"</span><span class="op">)</span>,</span>
<span> fill <span class="op">=</span> <span class="st">"interpretation"</span>, translate_ab <span class="op">=</span> <span class="st">"name"</span>, minimum <span class="op">=</span> <span class="fl">30</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">geom_sir</span><span class="op">(</span></span>
<span> position <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"antibiotic"</span>, <span class="st">"interpretation"</span><span class="op">)</span>,</span>
<span> fill <span class="op">=</span> <span class="st">"interpretation"</span>,</span>
<span> translate_ab <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> minimum <span class="op">=</span> <span class="fl">30</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">