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reference/mean_amr_distance.html
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@@ -7,7 +7,7 @@
<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="">2.1.1.9231</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</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">
@@ -71,23 +71,23 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a vector of class <a href="as.sir.html">sir</a>, <a href="as.mic.html">mic</a> or <a href="as.disk.html">disk</a>, or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns of any of these classes</p></dd>
<dd><p>A vector of class <a href="as.sir.html">sir</a>, <a href="as.mic.html">mic</a> or <a href="as.disk.html">disk</a>, or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns of any of these classes</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>variables to select (supports <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">tidyselect language</a> such as <code>column1:column4</code> and <code>where(is.mic)</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a></p></dd>
<dd><p>Variables to select. Supports <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">tidyselect language</a> (such as <code>column1:column4</code> and <code>where(is.mic)</code>), and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a></p></dd>
<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 input only consists of S+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 input only consists of S+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
<dt id="arg-amr-distance">amr_distance<a class="anchor" aria-label="anchor" href="#arg-amr-distance"></a></dt>
<dd><p>the outcome of <code>mean_amr_distance()</code></p></dd>
<dd><p>The outcome of <code>mean_amr_distance()</code></p></dd>
<dt id="arg-row">row<a class="anchor" aria-label="anchor" href="#arg-row"></a></dt>
<dd><p>an index, such as a row number</p></dd>
<dd><p>An index, such as a row number</p></dd>
</dl></div>
<div class="section level2">
@@ -160,10 +160,20 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> and "tobr"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12237407 -0.92897174 -0.07982527 0.24282355 0.22020411 0.34940813</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.12306945 0.80126097 0.09975463 -0.70395902</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span></span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in order(y$amr_distance):</span> argument 1 is not a vector</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 26 &lt;=1 0.5 -1.52288635</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 31 &lt;=1 8 -0.52427235</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 27 &gt;=4 0.5 -0.33703222</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 20 &gt;=4 0.5 -0.33703222</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 23 &gt;=4 1 -0.08737872</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 31 &gt;=4 2 0.16227477</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 30 &gt;=4 4 0.41192827</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 27 &gt;=4 4 0.41192827</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 20 &gt;=4 &gt;=16 0.91123527</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 27 &gt;=4 &gt;=16 0.91123527</span>
<span class="r-in"><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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>