Built site for AMR@2.1.1.9147: d94efb0

2025-07-12 14:21:57 +02:00 · 2025-02-14 13:23:46 +00:00
parent 97df961c58
commit 6d225ab56e
104 changed files with 489 additions and 503 deletions
--- a/reference/plot.html
+++ b/reference/plot.html
@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values

    <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="">2.1.1.9146</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9147</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">
@ -63,8 +63,6 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span></span>
 <span><span class="fu">scale_colour_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"edges"</span>, mic_range <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">scale_color_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"edges"</span>, mic_range <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
-<span></span>
 <span><span class="fu">scale_fill_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"edges"</span>, mic_range <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">scale_x_sir</span><span class="op">(</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>
@ -80,7 +78,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span>  <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for class 'mic'</span></span>
-<span><span class="fu">plot</span><span class="op">(</span><span class="va">x</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>,</span>
+<span><span class="fu">plot</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
 <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>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language</span>
 <span>  <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>, language <span class="op">=</span></span>
@ -91,8 +90,9 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span></span>
 <span><span class="co"># S3 method for class 'mic'</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 class="va">object</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  guideline <span class="op">=</span> <span class="st">"EUCAST"</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="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
+<span>  guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</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>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>,</span>
+<span>  language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>, language <span class="op">=</span></span>
 <span>  <span class="va">language</span><span class="op">)</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>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
@ -103,7 +103,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <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/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="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Disk diffusion diameter (mm)"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
-<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>,</span>
+<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="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</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>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
@ -113,8 +113,9 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <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">object</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</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>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>,</span>
 <span>  language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Disk diffusion diameter (mm)"</span>,</span>
-<span>  language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, guideline <span class="op">=</span> <span class="st">"EUCAST"</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>
-<span>  <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</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>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</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>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
 <span>  breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
@ -265,14 +266,14 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <h3 id="the-scale-mic-functions">The <code>scale_*_mic()</code> Functions<a class="anchor" aria-label="anchor" href="#the-scale-mic-functions"></a></h3>


-<p>The functions <code>scale_x_mic()</code>, <code>scale_y_mic()</code>, <code>scale_colour_mic()</code>, and <code>scale_fill_mic()</code> functions allow to plot the <a href="as.mic.html">mic</a> class (MIC values) on a continuous scale. They allow to rescale the MIC range, and retain the signs in MIC values if desired. Missing intermediate log2 levels will be plotted too.</p>
+<p>The functions <code>scale_x_mic()</code>, <code>scale_y_mic()</code>, <code>scale_colour_mic()</code>, and <code>scale_fill_mic()</code> functions allow to plot the <a href="as.mic.html">mic</a> class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the signs in MIC values if desired. Missing intermediate log2 levels will be plotted too.</p>
 </div>

 <div class="section">
 <h3 id="the-scale-sir-functions">The <code>scale_*_sir()</code> Functions<a class="anchor" aria-label="anchor" href="#the-scale-sir-functions"></a></h3>


-<p>The functions <code>scale_x_sir()</code>, <code>scale_colour_sir()</code>, and <code>scale_fill_sir()</code> functions allow to plot the <a href="as.sir.html">sir</a> class (S/I/R values). They can translate the S/I/R values to any of the 20 supported languages, and set colour-blind friendly colours to the <code>colour</code> and <code>fill</code> aesthetics.</p>
+<p>The functions <code>scale_x_sir()</code>, <code>scale_colour_sir()</code>, and <code>scale_fill_sir()</code> functions allow to plot the <a href="as.sir.html">sir</a> class in the right order (S &lt; SDD &lt; I &lt; R &lt; NI). At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the 20 supported languages (use <code>language = NULL</code> to keep S/I/R). Also, except for <code>scale_x_sir()</code>, they set colour-blind friendly colours to the <code>colour</code> and <code>fill</code> aesthetics.</p>
 </div>

 <div class="section">
@ -285,7 +286,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <li><p><code>theme_sir()</code> is a [ggplot2 theme][<code><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">ggplot2::theme()</a></code> with minimal distraction.</p></li>
 <li><p><code>labels_sir_count()</code> print datalabels on the bars with percentage and number of isolates, using <code><a href="https://ggplot2.tidyverse.org/reference/geom_text.html" class="external-link">ggplot2::geom_text()</a></code>.</p></li>
 </ul><p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
-<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 2024", "EUCAST 2023", "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2024", "CLSI 2023", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", and "CLSI 2011". Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
+<p>For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2024, unless the package option <code><a href="AMR-options.html">AMR_guideline</a></code> is set. See <code><a href="as.sir.html">as.sir()</a></code> for more information.</p>
 </div>

    </div>
@ -396,7 +397,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_x_sir</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> Apply <span style="background-color: #EEEEEE;">scale_x_sir()</span> to a variable of class 'sir', see <span style="background-color: #EEEEEE;">?as.sir</span>.</span>
+<span class="r-plt img"><img src="plot-15.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Plotting using scale_y_mic() and scale_colour_sir() ------------------</span></span></span>
@ -420,36 +421,36 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;">  • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
-<span class="r-plt img"><img src="plot-15.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-16.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="co"># and now with our MIC and SIR scale functions:</span></span></span>
 <span class="r-in"><span>  <span class="va">plain</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_y_mic</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_colour_sir</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> Apply <span style="background-color: #EEEEEE;">scale_colour_sir()</span> to a variable of class 'sir', see <span style="background-color: #EEEEEE;">?as.sir</span>.</span>
+<span class="r-plt img"><img src="plot-17.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="va">plain</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_y_mic</span><span class="op">(</span>mic_range <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">0.005</span>, <span class="fl">32</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"Our MICs!"</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_colour_sir</span><span class="op">(</span>language <span class="op">=</span> <span class="st">"el"</span>, eucast_I <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
 <span class="r-in"><span>                     name <span class="op">=</span> <span class="st">"In Greek!"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> Apply <span style="background-color: #EEEEEE;">scale_colour_sir()</span> to a variable of class 'sir', see <span style="background-color: #EEEEEE;">?as.sir</span>.</span>
+<span class="r-plt img"><img src="plot-18.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Plotting using ggplot2's autoplot() ----------------------------------</span></span></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_mic_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-16.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-19.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_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></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-17.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-20.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_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-18.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-21.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Plotting using scale_y_percent() -------------------------------------</span></span></span>
@ -470,9 +471,9 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><span>                    limits <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</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">theme_sir</span><span class="op">(</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-19.png" alt="" width="700" height="433"></span>
-<span class="r-plt img"><img src="plot-20.png" alt="" width="700" height="433"></span>
-<span class="r-plt img"><img src="plot-21.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-22.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-23.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-24.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
    </div>