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(v1.3.0.9016) mo_uncertainties() overhaul
2020-09-12 08:49:01 +02:00
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(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix
2020-09-18 16:05:53 +02:00
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(v1.3.0.9016) mo_uncertainties() overhaul
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(v1.4.0.9039) more unit tests
2020-12-13 20:44:32 +01:00
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(v1.3.0.9016) mo_uncertainties() overhaul
2020-09-12 08:49:01 +02:00
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<h1>Plotting for classes <code>rsi</code> and <code>disk</code></h1>
(v1.4.0.9037) random_* functions
2020-12-12 23:17:29 +01:00
<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>
(v1.3.0.9016) mo_uncertainties() overhaul
2020-09-12 08:49:01 +02:00
<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>
</div>
(v1.4.0.9037) random_* functions
2020-12-12 23:17:29 +01:00
<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>
(v1.4.0.9000) more extensive unit tests
2020-10-15 09:46:41 +02:00
<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>,
<span class='va'>...</span>
<span class='op'>)</span>
(v1.3.0.9016) mo_uncertainties() overhaul
2020-09-12 08:49:01 +02:00
<span class='co'># S3 method for mic</span>
(v1.4.0.9000) more extensive unit tests
2020-10-15 09:46:41 +02:00
<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>,
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>,
<span class='va'>...</span>
<span class='op'>)</span>
(v1.3.0.9016) mo_uncertainties() overhaul
2020-09-12 08:49:01 +02:00
<span class='co'># S3 method for rsi</span>
(v1.4.0.9000) more extensive unit tests
2020-10-15 09:46:41 +02:00
<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>
(v1.3.0.9016) mo_uncertainties() overhaul
2020-09-12 08:49:01 +02:00
<span class='co'># S3 method for rsi</span>
(v1.4.0.9000) more extensive unit tests
2020-10-15 09:46:41 +02:00
<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>
(v1.3.0.9016) mo_uncertainties() overhaul
2020-09-12 08:49:01 +02:00
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<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>
</tr>
<tr>
<th>main</th>
<td><p>overall and sub title for the plot.</p></td>
</tr>
<tr>
<th>ylab</th>
<td><p>a label for the y axis.</p></td>
</tr>
<tr>
<th>xlab</th>
<td><p>a label for the x axis.</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>
</tr>
<tr>
<th>...</th>
<td><p>Parameters passed on to functions</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>
</tr>
</table>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
(v1.4.0) matching score update
2020-10-08 11:16:03 +02:00
<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 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>
(v1.3.0.9016) mo_uncertainties() overhaul
2020-09-12 08:49:01 +02:00
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