P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-20 16:53:12 +02:00
Code Releases Activity

Built site for AMR: 2.1.1.9013@f2d245b

Browse Source
This commit is contained in:
github-actions
2024-03-03 22:05:59 +00:00
parent ab367558fe
commit 0b8e89c845
105 changed files with 341 additions and 327 deletions
Download Patch File Download Diff File Expand all files Collapse all files

54
reference/as.mic.html
View File

@ -10,7 +10,7 @@
<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="">2.1.1.9012</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9013</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">
@ -213,33 +213,33 @@
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>To interpret MIC values as SIR values, use <code><a href="as.sir.html">as.sir()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2023) and CLSI (2011-2023).</p>
<p>This class for MIC values is a quite a special data type: formally it is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with valid MIC values as <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>x <span class="ot">&lt;-</span> <span class="fu">random_mic</span>(<span class="dv">10</span>)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>x</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Class 'mic'</span></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] 16 1 8 8 64 &gt;=128 0.0625 32 32 16</span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="fu">is.factor</span>(x)</span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] TRUE</span></span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>x[<span class="dv">1</span>] <span class="sc">*</span> <span class="dv">2</span></span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] 32</span></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="fu">median</span>(x)</span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] 26</span></span></code></pre><p></p></div>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>x <span class="ot">&lt;-</span> <span class="fu">random_mic</span>(<span class="dv">10</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>x</span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; Class 'mic'</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="co">#&gt; [1] 16 1 8 8 64 &gt;=128 0.0625 32 32 16</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="fu">is.factor</span>(x)</span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a><span class="co">#&gt; [1] TRUE</span></span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a></span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a>x[<span class="dv">1</span>] <span class="sc">*</span> <span class="dv">2</span></span>
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a><span class="co">#&gt; [1] 32</span></span>
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a></span>
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a><span class="fu">median</span>(x)</span>
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a><span class="co">#&gt; [1] 26</span></span></code></pre><p></p></div>
<p>This makes it possible to maintain operators that often come with MIC values, such "&gt;=" and "&lt;=", even when filtering using <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> values in data analysis, e.g.:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>x[x <span class="sc">&gt;</span> <span class="dv">4</span>]</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Class 'mic'</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] 16 8 8 64 &gt;=128 32 32 16</span></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>df <span class="ot">&lt;-</span> <span class="fu">data.frame</span>(x, <span class="at">hospital =</span> <span class="st">"A"</span>)</span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="fu">subset</span>(df, x <span class="sc">&gt;</span> <span class="dv">4</span>) <span class="co"># or with dplyr: df %&gt;% filter(x &gt; 4)</span></span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; x hospital</span></span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 16 A</span></span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 5 64 A</span></span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 6 &gt;=128 A</span></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 8 32 A</span></span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 9 32 A</span></span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 10 16 A</span></span></code></pre><p></p></div>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>x[x <span class="sc">&gt;</span> <span class="dv">4</span>]</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; Class 'mic'</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; [1] 16 8 8 64 &gt;=128 32 32 16</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a>df <span class="ot">&lt;-</span> <span class="fu">data.frame</span>(x, <span class="at">hospital =</span> <span class="st">"A"</span>)</span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="fu">subset</span>(df, x <span class="sc">&gt;</span> <span class="dv">4</span>) <span class="co"># or with dplyr: df %&gt;% filter(x &gt; 4)</span></span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a><span class="co">#&gt; x hospital</span></span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a><span class="co">#&gt; 1 16 A</span></span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a><span class="co">#&gt; 5 64 A</span></span>
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a><span class="co">#&gt; 6 &gt;=128 A</span></span>
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a><span class="co">#&gt; 8 32 A</span></span>
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a><span class="co">#&gt; 9 32 A</span></span>
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a><span class="co">#&gt; 10 16 A</span></span></code></pre><p></p></div>
<p>All so-called <a href="https://rdrr.io/r/base/groupGeneric.html" class="external-link">group generic functions</a> are implemented for the MIC class (such as <code>!</code>, <code>!=</code>, <code>&lt;</code>, <code>&gt;=</code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp()</a></code>, <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2()</a></code>). Some functions of the <code>stats</code> package are also implemented (such as <code><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">quantile()</a></code>, <code><a href="https://rdrr.io/r/stats/median.html" class="external-link">median()</a></code>, <code><a href="https://rdrr.io/r/stats/fivenum.html" class="external-link">fivenum()</a></code>). Since <code><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd()</a></code> and <code><a href="https://rdrr.io/r/stats/cor.html" class="external-link">var()</a></code> are non-generic functions, these could not be extended. Use <code><a href="https://rdrr.io/r/stats/mad.html" class="external-link">mad()</a></code> as an alternative, or use e.g. <code>sd(as.numeric(x))</code> where <code>x</code> is your vector of MIC values.</p>
<p>Using <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> or <code><a href="https://rdrr.io/r/base/numeric.html" class="external-link">as.numeric()</a></code> on MIC values will remove the operators and return a numeric vector. Do <strong>not</strong> use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on MIC values as by the <span style="R">R</span> convention on <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a>s, it will return the index of the factor levels (which is often useless for regular users).</p>
<p>Use <code><a href="https://rdatatable.gitlab.io/data.table/reference/fdroplevels.html" class="external-link">droplevels()</a></code> to drop unused levels. At default, it will return a plain factor. Use <code>droplevels(..., as.mic = TRUE)</code> to maintain the <code>mic</code> class.</p>