(v1.5.0.9025) big plot and ggplot generics update

2025-07-10 05:41:59 +02:00 · 2021-02-25 10:33:08 +01:00
parent 31ceba5441
commit a673407904
42 changed files with 1058 additions and 842 deletions
--- a/docs/reference/as.mic.html
+++ b/docs/reference/as.mic.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9025</span>
      </span>
    </div>

@ -298,8 +298,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
       ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
       guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>

+<span class='co'># plot MIC values, see ?plot</span>
 <span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
+<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>mic_data</span>, mo <span class='op'>=</span> <span class='st'>"E. coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
 </pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
--- a/docs/reference/figures/lifecycle_tidyverse.svg
+++ b/docs/reference/figures/lifecycle_tidyverse.svg
@ -1,88 +1,32 @@
-<?xml version="1.0"?> <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
-"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> <svg
-xmlns="http://www.w3.org/2000/svg" xmlns:xl="http://www.w3.org/1999/xlink"
-version="1.1" viewBox="8 48 787 198" width="787pt" height="198pt"><metadata
-xmlns:dc="http://purl.org/dc/elements/1.1/"><dc:date>2018-01-05
-19:43Z</dc:date><!-- Produced by OmniGraffle Professional 5.4.4
--></metadata><defs><font-face font-family="Helvetica Neue" font-size="16"
-panose-1="2 0 5 3 0 0 0 2 0 4" units-per-em="1000" underline-position="-100"
-underline-thickness="50" slope="0" x-height="517" cap-height="714"
-ascent="951.99585" descent="-212.99744"
-font-weight="500"><font-face-src><font-face-name
-name="HelveticaNeue"/></font-face-src></font-face><marker orient="auto"
-overflow="visible" markerUnits="strokeWidth" id="FilledArrow_Marker" viewBox="-1
-4 10 8" markerWidth="10" markerHeight="8" color="black"><g><path d="M 8 0 L 0
-3 L 0 3 Z" fill="currentColor" stroke="currentColor"
-stroke-width="1"/></g></marker></defs><g stroke="none" stroke-opacity="1"
-stroke-dasharray="none" fill="none" fill-opacity="1"><title>Canvas
-1</title><rect fill="white" width="805.88977"
-height="536.27556"/><g><title>Layer 1</title><rect x="201.43709" y="148.91563"
-width="88.865815" height="36.026683" stroke="#0080ff" stroke-linecap="round"
-stroke-linejoin="round" stroke-width="2"/><text transform="translate(206.43709
-157.70498)" fill="black"><tspan font-family="Helvetica Neue" font-size="16"
-font-weight="500" x="7.8649073" y="15"
-textLength="63.136">maturing</tspan></text><rect x="10.4153" y="97.854194"
-width="123.69161" height="36.026683" stroke="#ff8000" stroke-linecap="round"
-stroke-linejoin="round" stroke-width="2"/><text transform="translate(15.4153
-106.643536)" fill="black"><tspan font-family="Helvetica Neue" font-size="16"
-font-weight="500" x="10.7658034" y="15"
-textLength="92.160004">experimental</tspan></text><rect x="339.64294"
-y="207.75286" width="64.848027" height="36.026683" stroke="green"
-stroke-linecap="round" stroke-linejoin="round" stroke-width="2"/><text
-transform="translate(344.64294 216.5422)" fill="black"><tspan
-font-family="Helvetica Neue" font-size="16" font-weight="500" x="5.7920134"
-y="15" textLength="43.264">stable</tspan></text><rect x="613.9284" y="118.27877"
-width="67.249806" height="36.026683" stroke="#ff8000" stroke-linecap="round"
-stroke-linejoin="round" stroke-width="2"/><text transform="translate(618.9284
-127.06811)" fill="black"><tspan font-family="Helvetica Neue" font-size="16"
-font-weight="500" x="5.9529028" y="15" textLength="5.328">r</tspan><tspan
-font-family="Helvetica Neue" font-size="16" font-weight="500" x="10.992903"
-y="15" textLength="22.511999">etir</tspan><tspan font-family="Helvetica Neue"
-font-size="16" font-weight="500" x="33.216903" y="15"
-textLength="18.08">ed</tspan></text><rect x="325.78587" y="50.19685"
-width="85.263146" height="36.026683" stroke="#0080ff" stroke-linecap="round"
-stroke-linejoin="round" stroke-width="2"/><text transform="translate(330.78587
-58.986193)" fill="black"><tspan font-family="Helvetica Neue" font-size="16"
-font-weight="500" x="7.543573" y="15"
-textLength="60.176">dormant</tspan></text><rect x="468.56405" y="142.10744"
-width="112.8836" height="36.026683" stroke="#0080ff" stroke-linecap="round"
-stroke-linejoin="round" stroke-width="2"/><text transform="translate(473.56405
-150.89678)" fill="black"><tspan font-family="Helvetica Neue" font-size="16"
-font-weight="500" x="9.801801" y="15"
-textLength="83.28">questioning</tspan></text><line x1="135.106906"
-y1="134.351596" x2="190.93937" y2="150.77291"
-marker-end="url(#FilledArrow_Marker)" stroke="black" stroke-linecap="round"
-stroke-linejoin="round" stroke-width="1"/><line x1="286.65074" y1="185.94232"
-x2="329.67024" y2="205.99944" marker-end="url(#FilledArrow_Marker)"
-stroke="black" stroke-linecap="round" stroke-linejoin="round"
-stroke-width="1"/><path d="M 379.93472 206.75285 C 387.55754 192.63012 401.66897
-174.0594 426.21202 163.52488 C 436.33446 159.18006 447.11932 156.67954 457.70464
-155.39871" marker-end="url(#FilledArrow_Marker)" stroke="black"
-stroke-linecap="round" stroke-linejoin="round" stroke-width="1"/><line
-x1="582.44766" y1="148.95154" x2="603.2104" y2="144.91434"
-marker-end="url(#FilledArrow_Marker)" stroke="black" stroke-linecap="round"
-stroke-linejoin="round" stroke-width="1"/><path d="M 501.44774 179.13413 C
-487.32306 189.48841 467.98586 202.01855 446.6366 211.18222 C 435.19097 216.09499
-424.5888 219.42992 415.18313 221.6778" marker-end="url(#FilledArrow_Marker)"
-stroke="black" stroke-linecap="round" stroke-linejoin="round"
-stroke-width="1"/><path d="M 412.04903 66.0841 C 438.72737 66.23414 475.24547
-68.794908 514.7185 78.42248 C 552.22946 87.57149 584.04206 101.061534 607.12235
-112.71587" marker-end="url(#FilledArrow_Marker)" stroke="black"
-stroke-linecap="round" stroke-linejoin="round" stroke-width="1"/><path d="M
-135.10692 119.41541 C 165.84715 119.854806 204.35783 118.583695 242.39084
-112.46344 C 276.08222 107.04184 303.03701 98.838735 323.23284 90.96218"
-marker-end="url(#FilledArrow_Marker)" stroke="black" stroke-linecap="round"
-stroke-linejoin="round" stroke-width="1"/><path d="M 324.78586 66.603523 C
-301.6689 66.933135 270.15767 68.9068 232.17855 75.018384 C 200.11208 80.178506
-169.19774 87.361075 143.238715 94.26646" marker-end="url(#FilledArrow_Marker)"
-stroke="black" stroke-linecap="round" stroke-linejoin="round"
-stroke-width="1"/><rect x="707.0446" y="118.27877" width="85.263146"
-height="36.026683" stroke="red" stroke-linecap="round" stroke-linejoin="round"
-stroke-width="2"/><text transform="translate(712.0446 127.06811)"
-fill="black"><tspan font-family="Helvetica Neue" font-size="16"
-font-weight="500" x="7.255573" y="15" textLength="13.92">ar</tspan><tspan
-font-family="Helvetica Neue" font-size="16" font-weight="500" x="20.887573"
-y="15" textLength="47.12">chived</tspan></text><line x1="682.1782"
-y1="136.29211" x2="696.1446" y2="136.29211"
-marker-end="url(#FilledArrow_Marker)" stroke="black" stroke-linecap="round"
-stroke-linejoin="round" stroke-width="1"/></g></g></svg>
+<?xml version="1.0" encoding="UTF-8"?>
+<svg width="510.24pt" height="184.25pt" version="1.1" viewBox="0 0 510.24 184.25" xmlns="http://www.w3.org/2000/svg">
+<style>
+  text {
+    fill: white;
+    font-family: "Helvetica Neue";
+  }
+</style>
+<defs>
+<marker id="a" color="black" overflow="visible" markerHeight="6" markerWidth="7" orient="auto" viewBox="-1 -3 7 6">
+<path d="m4.8 0-4.8-1.8v3.6z" fill="currentColor" stroke="currentColor"/>
+</marker>
+</defs>
+<g fill="none">
+<title>Canvas 1</title>
+<rect width="510.24" height="184.25" fill="#fff"/>
+<g>
+<title>Layer 1</title>
+<rect x="5.6693" y="5.6693" width="116.22" height="48.189" fill="#fd8008"/>
+<text transform="translate(63.7793 29.7638)" dominant-baseline="middle" text-anchor="middle">experimental</text>
+<rect x="161.57" y="113.39" width="150.24" height="68.031" fill="#108001"/>
+<text transform="translate(236.69 147.4055)" dominant-baseline="middle" text-anchor="middle" font-size="19">stable</text>
+<path d="m63.356 53.858c2.0388 19.203 10.427 45.968 38.691 65.197 13.679 9.3061 30.217 15.625 46.951 19.9" marker-end="url(#a)" stroke="#000" stroke-linecap="round" stroke-linejoin="round" stroke-width="2"/>
+<path d="m311.81 131.57c18.392-5.7638 38.128-13.509 56.693-23.85 25.216-14.046 43.275-30.1 55.731-43.973" marker-end="url(#a)" stroke="#000" stroke-linecap="round" stroke-linejoin="round" stroke-width="2"/>
+<rect x="391.18" y="119.06" width="113.39" height="48.189" fill="#074080"/>
+<text transform="translate(447.875 143.1545)" dominant-baseline="middle" text-anchor="middle">superseded</text>
+<line x1="311.81" x2="378.29" y1="147.22" y2="145.23" marker-end="url(#a)" stroke="#000" stroke-linecap="round" stroke-linejoin="round" stroke-width="2"/>
+<rect x="391.18" y="5.6693" width="113.39" height="48.189" fill="#fd8008"/>
+<text transform="translate(447.875 29.7638)" dominant-baseline="middle" text-anchor="middle">deprecated</text>
+</g>
+</g>
+</svg>
--- a/docs/reference/ggplot_rsi.html
+++ b/docs/reference/ggplot_rsi.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9025</span>
      </span>
    </div>

@ -286,8 +286,9 @@
 <span class='fu'>scale_y_percent</span><span class='op'>(</span>breaks <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>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>, limits <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>

 <span class='fu'>scale_rsi_colours</span><span class='op'>(</span>
-  colours <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>S <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, SI <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, I <span class='op'>=</span> <span class='st'>"#61f7ff"</span>, IR <span class='op'>=</span> <span class='st'>"#ff6961"</span>, R <span class='op'>=</span>
-    <span class='st'>"#ff6961"</span><span class='op'>)</span>
+  colours <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>S <span class='op'>=</span> <span class='st'>"#3CAEA3"</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>, R <span class='op'>=</span>
+    <span class='st'>"#ED553B"</span><span class='op'>)</span>,
+  aesthetics <span class='op'>=</span> <span class='st'>"fill"</span>
 <span class='op'>)</span>

 <span class='fu'>theme_rsi</span><span class='op'>(</span><span class='op'>)</span>
@ -361,7 +362,7 @@
    </tr>
    <tr>
      <th>colours</th>
-      <td><p>a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be <code>FALSE</code> to use default <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> colours.</p></td>
+      <td><p>a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be <code>FALSE</code> for standard <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> colours. The default colours are colour-blind friendly.</p></td>
    </tr>
    <tr>
      <th>datalabels</th>
@ -399,6 +400,10 @@
      <th>...</th>
      <td><p>other arguments passed on to <code>geom_rsi()</code></p></td>
    </tr>
+    <tr>
+      <th>aesthetics</th>
+      <td><p>aesthetics to apply the colours to, defaults to "fill" but can also be "colour" or "both"</p></td>
+    </tr>
    </table>

    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9025</span>
      </span>
    </div>

@ -453,7 +453,7 @@
      </tr><tr>
        
        <td>
-          <p><code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">barplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">barplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
+          <p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> </p>
        </td>
        <td><p>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></p></td>
      </tr><tr>
--- a/docs/reference/like.html
+++ b/docs/reference/like.html
@ -49,7 +49,7 @@
  <script src="../extra.js"></script>

 <meta property="og:title" content="Pattern Matching with Keyboard Shortcut — like" />
-<meta property="og:description" content="Convenient wrapper around grep() to match a pattern: x %like% pattern. It always returns a logical vector and is always case-insensitive (use x %like_case% pattern for case-sensitive matching). Also, pattern can be as long as x to compare items of each index in both vectors, or they both can have the same length to iterate over all cases." />
+<meta property="og:description" content="Convenient wrapper around grepl() to match a pattern: x %like% pattern. It always returns a logical vector and is always case-insensitive (use x %like_case% pattern for case-sensitive matching). Also, pattern can be as long as x to compare items of each index in both vectors, or they both can have the same length to iterate over all cases." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />


@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9025</span>
      </span>
    </div>

@ -239,7 +239,7 @@
    </div>

    <div class="ref-description">
-    <p>Convenient wrapper around <code><a href='https://rdrr.io/r/base/grep.html'>grep()</a></code> to match a pattern: <code>x %like% pattern</code>. It always returns a <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector and is always case-insensitive (use <code>x %like_case% pattern</code> for case-sensitive matching). Also, <code>pattern</code> can be as long as <code>x</code> to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.</p>
+    <p>Convenient wrapper around <code><a href='https://rdrr.io/r/base/grep.html'>grepl()</a></code> to match a pattern: <code>x %like% pattern</code>. It always returns a <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector and is always case-insensitive (use <code>x %like_case% pattern</code> for case-sensitive matching). Also, <code>pattern</code> can be as long as <code>x</code> to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.</p>
    </div>

    <pre class="usage"><span class='fu'>like</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>pattern</span>, ignore.case <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
@ -295,7 +295,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>

-    <div class='dont-index'><p><code><a href='https://rdrr.io/r/base/grep.html'>grep()</a></code></p></div>
+    <div class='dont-index'><p><code><a href='https://rdrr.io/r/base/grep.html'>grepl()</a></code></p></div>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><span class='co'># simple test</span>
@ -306,11 +306,15 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='va'>b</span> <span class='op'>%like%</span> <span class='va'>a</span>
 <span class='co'>#&gt; FALSE</span>

-<span class='co'># also supports multiple patterns, length must be equal to x</span>
+<span class='co'># also supports multiple patterns</span>
 <span class='va'>a</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Test case"</span>, <span class='st'>"Something different"</span>, <span class='st'>"Yet another thing"</span><span class='op'>)</span>
 <span class='va'>b</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>     <span class='st'>"case"</span>,           <span class='st'>"diff"</span>,      <span class='st'>"yet"</span><span class='op'>)</span>
 <span class='va'>a</span> <span class='op'>%like%</span> <span class='va'>b</span>
 <span class='co'>#&gt; TRUE TRUE TRUE</span>
+<span class='va'>a</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>]</span> <span class='op'>%like%</span> <span class='va'>b</span>
+<span class='co'>#&gt; TRUE FALSE FALSE</span>
+<span class='va'>a</span> <span class='op'>%like%</span> <span class='va'>b</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>]</span>
+<span class='co'>#&gt; TRUE FALSE FALSE</span>

 <span class='co'># get isolates whose name start with 'Ent' or 'ent'</span>
 <span class='co'># \donttest{</span>
--- a/docs/reference/plot.html
+++ b/docs/reference/plot.html
@ -49,7 +49,7 @@
  <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 print classes of the AMR package." />
+<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.png" />


@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9025</span>
      </span>
    </div>

@ -234,65 +234,78 @@
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></h1>
-    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/disk.R'><code>R/disk.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a>, and 1 more</small>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/plot.R'><code>R/plot.R</code></a></small>
    <div class="hidden name"><code>plot.Rd</code></div>
    </div>

    <div class="ref-description">
-    <p>Functions to print classes of the <code>AMR</code> package.</p>
+    <p>Functions to plot classes <code>rsi</code>, <code>mic</code> and <code>disk</code>, with support for base R and <code>ggplot2</code>.</p>
    </div>

-    <pre class="usage"><span class='co'># S3 method for disk</span>
-<span class='fu'>plot</span><span class='op'>(</span>
-  <span class='va'>x</span>,
-  main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
-  ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
-  xlab <span class='op'>=</span> <span class='st'>"Disk diffusion (mm)"</span>,
-  axes <span class='op'>=</span> <span class='cn'>FALSE</span>,
-  <span class='va'>...</span>
-<span class='op'>)</span>
-
-<span class='co'># S3 method for mic</span>
+    <pre class="usage"><span class='co'># S3 method for mic</span>
 <span class='fu'>plot</span><span class='op'>(</span>
  <span class='va'>x</span>,
  main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
  ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
-  xlab <span class='op'>=</span> <span class='st'>"MIC value"</span>,
-  axes <span class='op'>=</span> <span class='cn'>FALSE</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Minimum Inhibitory Concentration (mg/L)"</span>,
+  mo <span class='op'>=</span> <span class='cn'>NULL</span>,
+  ab <span class='op'>=</span> <span class='cn'>NULL</span>,
+  guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
+  colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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>,
+  expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
  <span class='va'>...</span>
 <span class='op'>)</span>

 <span class='co'># S3 method for mic</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span><span class='op'>(</span>
-  <span class='va'>height</span>,
-  main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>height</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
+<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
+  <span class='va'>data</span>,
+  mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
+  title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
  ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
-  xlab <span class='op'>=</span> <span class='st'>"MIC value"</span>,
-  axes <span class='op'>=</span> <span class='cn'>FALSE</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Minimum Inhibitory Concentration (mg/L)"</span>,
+  mo <span class='op'>=</span> <span class='cn'>NULL</span>,
+  ab <span class='op'>=</span> <span class='cn'>NULL</span>,
+  guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
+  colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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>,
+  expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span>
+
+<span class='co'># S3 method for disk</span>
+<span class='fu'>plot</span><span class='op'>(</span>
+  <span class='va'>x</span>,
+  main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
+  ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Disk diffusion diameter (mm)"</span>,
+  mo <span class='op'>=</span> <span class='cn'>NULL</span>,
+  ab <span class='op'>=</span> <span class='cn'>NULL</span>,
+  guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
+  colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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>,
+  expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span>
+
+<span class='co'># S3 method for disk</span>
+<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
+  <span class='va'>data</span>,
+  mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
+  title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
+  ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Disk diffusion diameter (mm)"</span>,
+  mo <span class='op'>=</span> <span class='cn'>NULL</span>,
+  ab <span class='op'>=</span> <span class='cn'>NULL</span>,
+  guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
+  colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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>,
+  expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
  <span class='va'>...</span>
 <span class='op'>)</span>

 <span class='co'># S3 method for rsi</span>
 <span class='fu'>plot</span><span class='op'>(</span>
  <span class='va'>x</span>,
-  lwd <span class='op'>=</span> <span class='fl'>2</span>,
-  ylim <span class='op'>=</span> <span class='cn'>NULL</span>,
  ylab <span class='op'>=</span> <span class='st'>"Percentage"</span>,
  xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
  main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
-  axes <span class='op'>=</span> <span class='cn'>FALSE</span>,
-  <span class='va'>...</span>
-<span class='op'>)</span>
-
-<span class='co'># S3 method for rsi</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span><span class='op'>(</span>
-  <span class='va'>height</span>,
-  col <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"chartreuse4"</span>, <span class='st'>"chartreuse3"</span>, <span class='st'>"brown3"</span><span class='op'>)</span>,
-  xlab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>beside</span>, <span class='st'>"Antimicrobial Interpretation"</span>, <span class='st'>""</span><span class='op'>)</span>,
-  main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>height</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
-  ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
-  beside <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  axes <span class='op'>=</span> <span class='va'>beside</span>,
  <span class='va'>...</span>
 <span class='op'>)</span></pre>

@ -301,62 +314,53 @@
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>x</th>
-      <td><p>the coordinates of points in the plot. Alternatively, a
-      single plotting structure, function or <em>any <span style="R">R</span> object with a
-        <code>plot</code> method</em> can be provided.</p></td>
+      <td><p>MIC values created with <code><a href='as.mic.html'>as.mic()</a></code> or disk diffusion values created with <code><a href='as.disk.html'>as.disk()</a></code></p></td>
    </tr>
    <tr>
-      <th>main</th>
-      <td><p>overall and sub title for the plot.</p></td>
+      <th>main, title</th>
+      <td><p>title of the plot</p></td>
    </tr>
    <tr>
-      <th>ylab</th>
-      <td><p>a label for the y axis.</p></td>
+      <th>xlab, ylab</th>
+      <td><p>axis title</p></td>
    </tr>
    <tr>
-      <th>xlab</th>
-      <td><p>a label for the x axis.</p></td>
+      <th>mo</th>
+      <td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code></p></td>
    </tr>
    <tr>
-      <th>axes</th>
-      <td><p>logical.  If <code>TRUE</code>, a vertical (or horizontal, if
-    <code>horiz</code> is true) axis is drawn.</p></td>
+      <th>ab</th>
+      <td><p>any (vector of) text that can be coerced to a valid antimicrobial code with <code><a href='as.ab.html'>as.ab()</a></code></p></td>
+    </tr>
+    <tr>
+      <th>guideline</th>
+      <td><p>interpretation guideline to use, defaults to the latest included EUCAST guideline, see <em>Details</em></p></td>
+    </tr>
+    <tr>
+      <th>colours_RSI</th>
+      <td><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></td>
+    </tr>
+    <tr>
+      <th>expand</th>
+      <td><p>logical to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.</p></td>
    </tr>
    <tr>
      <th>...</th>
-      <td><p>Arguments passed on to functions</p></td>
+      <td><p>arguments passed on to <code><a href='as.rsi.html'>as.rsi()</a></code></p></td>
    </tr>
    <tr>
-      <th>height</th>
-      <td><p>either a vector or matrix of values describing the
-    bars which make up the plot.  If <code>height</code> is a vector, the
-    plot consists of a sequence of rectangular bars with heights
-    given by the values in the vector.  If <code>height</code> is a matrix
-    and <code>beside</code> is <code>FALSE</code> then each bar of the plot
-    corresponds to a column of <code>height</code>, with the values in the
-    column giving the heights of stacked sub-bars making up the
-    bar.  If <code>height</code> is a matrix and <code>beside</code> is
-    <code>TRUE</code>, then the values in each column are juxtaposed
-    rather than stacked.</p></td>
-    </tr>
-    <tr>
-      <th>ylim</th>
-      <td><p>limits for the y axis.</p></td>
-    </tr>
-    <tr>
-      <th>col</th>
-      <td><p>a vector of colors for the bars or bar components.
-    By default, grey is used if <code>height</code> is a vector, and a
-    gamma-corrected grey palette if <code>height</code> is a matrix.</p></td>
-    </tr>
-    <tr>
-      <th>beside</th>
-      <td><p>a logical value.  If <code>FALSE</code>, the columns of
-    <code>height</code> are portrayed as stacked bars, and if <code>TRUE</code>
-    the columns are portrayed as juxtaposed bars.</p></td>
+      <th>mapping</th>
+      <td><p>aesthetic mappings to use for <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot()</a></code></p></td>
    </tr>
    </table>

+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>The <code>ggplot</code> functions return a <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> model that is extendible with any <code>ggplot2</code> function.</p>
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
+<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>

    
@ -370,6 +374,22 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s

 <p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>

+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><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 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 class='fu'>plot</span><span class='op'>(</span><span class='va'>some_mic_values</span><span class='op'>)</span>
+<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_disk_values</span><span class='op'>)</span>
+
+<span class='co'># when providing the microorganism and antibiotic, colours will show interpretations:</span>
+<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_mic_values</span>, mo <span class='op'>=</span> <span class='st'>"S. aureus"</span>, ab <span class='op'>=</span> <span class='st'>"ampicillin"</span><span class='op'>)</span>
+<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_disk_values</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 class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
+  <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_mic_values</span><span class='op'>)</span>
+  <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_disk_values</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 class='op'>}</span>
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
--- a/docs/reference/random.html
+++ b/docs/reference/random.html
@ -49,7 +49,7 @@
  <script src="../extra.js"></script>

 <meta property="og:title" content="Random MIC Values/Disk Zones/RSI Generation — random" />
-<meta property="og:description" content="These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice." />
+<meta property="og:description" content="These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />


@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9025</span>
      </span>
    </div>

@ -239,7 +239,7 @@
    </div>

    <div class="ref-description">
-    <p>These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice.</p>
+    <p>These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.</p>
    </div>

    <pre class="usage"><span class='fu'>random_mic</span><span class='op'>(</span><span class='va'>size</span>, mo <span class='op'>=</span> <span class='cn'>NULL</span>, ab <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>