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@ -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="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</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">
@ -161,7 +161,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to methods</p></dd>
<dd><p>Arguments passed on to methods.</p></dd>
<dt id="arg-colours-sir">colours_SIR<a class="anchor" aria-label="anchor" href="#arg-colours-sir"></a></dt>
@ -177,27 +177,27 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg-x-object">x, object<a class="anchor" aria-label="anchor" href="#arg-x-object"></a></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.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>
<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 id="arg-mo">mo<a class="anchor" aria-label="anchor" href="#arg-mo"></a></dt>
<dd><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></dd>
<dd><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></dd>
<dt id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></dt>
<dd><p>Any (vector of) text that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dd><p>Any (vector of) text that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>Interpretation guideline to use - the default is the latest included EUCAST guideline, see <em>Details</em></p></dd>
<dd><p>Interpretation guideline to use - the default is the latest included EUCAST guideline, see <em>Details</em>.</p></dd>
<dt id="arg-main-title">main, title<a class="anchor" aria-label="anchor" href="#arg-main-title"></a></dt>
<dd><p>Title of the plot</p></dd>
<dd><p>Title of the plot.</p></dd>
<dt id="arg-xlab-ylab">xlab, ylab<a class="anchor" aria-label="anchor" href="#arg-xlab-ylab"></a></dt>
<dd><p>Axis title</p></dd>
<dd><p>Axis title.</p></dd>
<dt id="arg-expand">expand<a class="anchor" aria-label="anchor" href="#arg-expand"></a></dt>
@ -213,31 +213,31 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg-facet">facet<a class="anchor" aria-label="anchor" href="#arg-facet"></a></dt>
<dd><p>Variable to split plots by, either <code>"interpretation"</code> (default) or <code>"antibiotic"</code> or a grouping variable</p></dd>
<dd><p>Variable to split plots by, either <code>"interpretation"</code> (default) or <code>"antibiotic"</code> or a grouping variable.</p></dd>
<dt id="arg-nrow">nrow<a class="anchor" aria-label="anchor" href="#arg-nrow"></a></dt>
<dd><p>(when using <code>facet</code>) number of rows</p></dd>
<dd><p>(when using <code>facet</code>) number of rows.</p></dd>
<dt id="arg-breaks">breaks<a class="anchor" aria-label="anchor" href="#arg-breaks"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of positions</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of positions.</p></dd>
<dt id="arg-limits">limits<a class="anchor" aria-label="anchor" href="#arg-limits"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of length two providing limits of the scale, use <code>NA</code> to refer to the existing minimum or maximum</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of length two providing limits of the scale, use <code>NA</code> to refer to the existing minimum or maximum.</p></dd>
<dt id="arg-aesthetics">aesthetics<a class="anchor" aria-label="anchor" href="#arg-aesthetics"></a></dt>
<dd><p>Aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"</p></dd>
<dd><p>Aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size".</p></dd>
<dt id="arg-position">position<a class="anchor" aria-label="anchor" href="#arg-position"></a></dt>
<dd><p>Position adjustment of bars, either <code>"fill"</code>, <code>"stack"</code> or <code>"dodge"</code></p></dd>
<dd><p>Position adjustment of bars, either <code>"fill"</code>, <code>"stack"</code> or <code>"dodge"</code>.</p></dd>
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>A column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dd><p>A column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code>.</p></dd>
<dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt>
@ -245,15 +245,15 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code>.</p></dd>
<dt id="arg-datalabels-size">datalabels.size<a class="anchor" aria-label="anchor" href="#arg-datalabels-size"></a></dt>
<dd><p>Size of the datalabels</p></dd>
<dd><p>Size of the datalabels.</p></dd>
<dt id="arg-datalabels-colour">datalabels.colour<a class="anchor" aria-label="anchor" href="#arg-datalabels-colour"></a></dt>
<dd><p>Colour of the datalabels</p></dd>
<dd><p>Colour of the datalabels.</p></dd>
</dl></div>
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