Built site for AMR: 1.8.2.9096@98e62c9

2025-09-05 02:09:37 +02:00 · 2023-01-21 22:53:21 +00:00
parent d18dc71c10
commit e289d2568d
114 changed files with 1380 additions and 1308 deletions
--- a/reference/plot.html
+++ b/reference/plot.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- 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"><meta name="description" content="Functions to plot classes rsi, mic and disk, with support for base R and ggplot2."><title>Plotting for Classes rsi, mic and disk — plot • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><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-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Plotting for Classes rsi, mic and disk — plot"><meta property="og:description" content="Functions to plot classes rsi, mic and disk, with support for base R and ggplot2."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- 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"><meta name="description" content="Functions to plot classes sir, mic and disk, with support for base R and ggplot2."><title>Plotting for Classes sir, mic and disk — plot • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><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-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Plotting for Classes sir, mic and disk — plot"><meta property="og:description" content="Functions to plot classes sir, mic and disk, with support for base R and ggplot2."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
@@ -10,7 +10,7 @@
    
    <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="">1.8.2.9095</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</small>

    
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -127,13 +127,13 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.svg" class="logo" alt=""><h1>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Plotting for Classes <code>sir</code>, <code>mic</code> and <code>disk</code></h1>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/plot.R" class="external-link"><code>R/plot.R</code></a></small>
      <div class="d-none name"><code>plot.Rd</code></div>
    </div>

    <div class="ref-description section level2">
-    <p>Functions to plot classes <code>rsi</code>, <code>mic</code> and <code>disk</code>, with support for base <span style="R">R</span> and <code>ggplot2</code>.</p>
+    <p>Functions to plot classes <code>sir</code>, <code>mic</code> and <code>disk</code>, with support for base <span style="R">R</span> and <code>ggplot2</code>.</p>
    </div>

    <div class="section level2">
@@ -147,7 +147,7 @@
 <span>  main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>  ylab <span class="op">=</span> <span class="st">"Frequency"</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>,</span>
-<span>  colours_RSI <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">"#ED553B"</span>, <span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span><span class="op">)</span>,</span>
+<span>  colours_SIR <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">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</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>  expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  <span class="va">...</span></span>
@@ -162,7 +162,7 @@
 <span>  title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>  ylab <span class="op">=</span> <span class="st">"Frequency"</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>,</span>
-<span>  colours_RSI <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">"#ED553B"</span>, <span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span><span class="op">)</span>,</span>
+<span>  colours_SIR <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">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</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>  expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  <span class="va">...</span></span>
@@ -180,7 +180,7 @@
 <span>  mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  ab <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  guideline <span class="op">=</span> <span class="st">"EUCAST"</span>,</span>
-<span>  colours_RSI <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">"#ED553B"</span>, <span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span><span class="op">)</span>,</span>
+<span>  colours_SIR <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">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</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>  expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  <span class="va">...</span></span>
@@ -195,7 +195,7 @@
 <span>  ylab <span class="op">=</span> <span class="st">"Frequency"</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="st">"Disk diffusion diameter (mm)"</span>,</span>
 <span>  guideline <span class="op">=</span> <span class="st">"EUCAST"</span>,</span>
-<span>  colours_RSI <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">"#ED553B"</span>, <span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span><span class="op">)</span>,</span>
+<span>  colours_SIR <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">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</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>  expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  <span class="va">...</span></span>
@@ -204,7 +204,7 @@
 <span><span class="co"># S3 method for disk</span></span>
 <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S3 method for rsi</span></span>
+<span><span class="co"># S3 method for sir</span></span>
 <span><span class="fu">plot</span><span class="op">(</span></span>
 <span>  <span class="va">x</span>,</span>
 <span>  ylab <span class="op">=</span> <span class="st">"Percentage"</span>,</span>
@@ -214,25 +214,25 @@
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S3 method for rsi</span></span>
+<span><span class="co"># S3 method for sir</span></span>
 <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span></span>
 <span>  <span class="va">object</span>,</span>
 <span>  title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="st">"Antimicrobial Interpretation"</span>,</span>
 <span>  ylab <span class="op">=</span> <span class="st">"Frequency"</span>,</span>
-<span>  colours_RSI <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">"#ED553B"</span>, <span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span><span class="op">)</span>,</span>
+<span>  colours_SIR <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">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</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>  <span class="va">...</span></span>
 <span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S3 method for rsi</span></span>
+<span><span class="co"># S3 method for sir</span></span>
 <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
    </div>

    <div class="section level2">
    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
    <dl><dt>x, object</dt>
-<dd><p>values created with <code><a href="as.mic.html">as.mic()</a></code>, <code><a href="as.disk.html">as.disk()</a></code> or <code><a href="as.rsi.html">as.rsi()</a></code> (or their <code>random_*</code> variants, such as <code><a href="random.html">random_mic()</a></code>)</p></dd>
+<dd><p>values created with <code><a href="as.mic.html">as.mic()</a></code>, <code><a href="as.disk.html">as.disk()</a></code> or <code><a href="as.sir.html">as.sir()</a></code> (or their <code>random_*</code> variants, such as <code><a href="random.html">random_mic()</a></code>)</p></dd>


 <dt>mo</dt>
@@ -255,8 +255,8 @@
 <dd><p>axis title</p></dd>


-<dt>colours_RSI</dt>
-<dd><p>colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.</p></dd>
+<dt>colours_SIR</dt>
+<dd><p>colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). The default colours are colour-blind friendly.</p></dd>


 <dt>language</dt>
@@ -291,13 +291,13 @@
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">some_mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">some_disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">some_rsi_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_rsi</a></span><span class="op">(</span><span class="fl">50</span>, prob_RSI <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="fl">0.30</span>, <span class="fl">0.55</span>, <span class="fl">0.05</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">some_sir_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">50</span>, prob_SIR <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="fl">0.55</span>, <span class="fl">0.05</span>, <span class="fl">0.30</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_mic_values</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="plot-1.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="plot-2.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_rsi_values</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_sir_values</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="plot-3.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># when providing the microorganism and antibiotic, colours will show interpretations:</span></span></span>
@@ -318,7 +318,7 @@
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-plt img"><img src="plot-8.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
-<span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_rsi_values</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_sir_values</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>