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<h1>(Key) Antimicrobials for First Weighted Isolates</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/key_antimicrobials.R" class="external-link"><code>R/key_antimicrobials.R</code></a></small>
<div class="hidden name"><code>key_antimicrobials.Rd</code></div>
</div>
<div class="ref-description">
<p>These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see <code><a href="first_isolate.html">first_isolate()</a></code>). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">key_antimicrobials</span><span class="op">(</span></span>
<span> x <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> universal <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">"ampicillin"</span>, <span class="st">"amoxicillin/clavulanic acid"</span>, <span class="st">"cefuroxime"</span>,</span>
<span> <span class="st">"piperacillin/tazobactam"</span>, <span class="st">"ciprofloxacin"</span>, <span class="st">"trimethoprim/sulfamethoxazole"</span><span class="op">)</span>,</span>
<span> gram_negative <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">"gentamicin"</span>, <span class="st">"tobramycin"</span>, <span class="st">"colistin"</span>, <span class="st">"cefotaxime"</span>, <span class="st">"ceftazidime"</span>,</span>
<span> <span class="st">"meropenem"</span><span class="op">)</span>,</span>
<span> gram_positive <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">"vancomycin"</span>, <span class="st">"teicoplanin"</span>, <span class="st">"tetracycline"</span>, <span class="st">"erythromycin"</span>,</span>
<span> <span class="st">"oxacillin"</span>, <span class="st">"rifampin"</span><span class="op">)</span>,</span>
<span> antifungal <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">"anidulafungin"</span>, <span class="st">"caspofungin"</span>, <span class="st">"fluconazole"</span>, <span class="st">"miconazole"</span>, <span class="st">"nystatin"</span>,</span>
<span> <span class="st">"voriconazole"</span><span class="op">)</span>,</span>
<span> only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">all_antimicrobials</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">antimicrobials_equal</span><span class="op">(</span></span>
<span> <span class="va">y</span>,</span>
<span> <span class="va">z</span>,</span>
<span> type <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">"points"</span>, <span class="st">"keyantimicrobials"</span><span class="op">)</span>,</span>
<span> ignore_I <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> points_threshold <span class="op">=</span> <span class="fl">2</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with antibiotics columns, like <code>AMX</code> or <code>amox</code>. Can be left blank to determine automatically</p></dd>
<dt>col_mo</dt>
<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>universal</dt>
<dd><p>names of <strong>broad-spectrum</strong> antimicrobial agents, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
<dt>gram_negative</dt>
<dd><p>names of antibiotic agents for <strong>Gram-positives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
<dt>gram_positive</dt>
<dd><p>names of antibiotic agents for <strong>Gram-negatives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
<dt>antifungal</dt>
<dd><p>names of antifungal agents for <strong>fungi</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></dd>
<dt>only_rsi_columns</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>&lt;rsi&gt;</code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
<dt>...</dt>
<dd><p>ignored, only in place to allow future extensions</p></dd>
<dt>y, z</dt>
<dd><p><a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vectors to compare</p></dd>
<dt>type</dt>
<dd><p>type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em></p></dd>
<dt>ignore_I</dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></dd>
<dt>points_threshold</dt>
<dd><p>minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></dd>
</dl></div>
<div id="details">
<h2>Details</h2>
<p>The <code>key_antimicrobials()</code> and <code>all_antimicrobials()</code> functions are context-aware. This means that the <code>x</code> argument can be left blank if used inside a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> call, see <em>Examples</em>.</p>
<p>The function <code>key_antimicrobials()</code> returns a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector with 12 antimicrobial results for every isolate. The function <code>all_antimicrobials()</code> returns a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector with all antimicrobial results for every isolate. These vectors can then be compared using <code>antimicrobials_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antimicrobials()</code> and ignored by <code>antimicrobials_equal()</code>.</p>
<p>Please see the <code><a href="first_isolate.html">first_isolate()</a></code> function how these important functions enable the 'phenotype-based' method for determination of first isolates.</p>
<p>The default antimicrobial agents used for <strong>all rows</strong> (set in <code>universal</code>) are:</p><ul><li><p>Ampicillin</p></li>
<li><p>Amoxicillin/clavulanic acid</p></li>
<li><p>Cefuroxime</p></li>
<li><p>Ciprofloxacin</p></li>
<li><p>Piperacillin/tazobactam</p></li>
<li><p>Trimethoprim/sulfamethoxazole</p></li>
</ul><p>The default antimicrobial agents used for <strong>Gram-negative bacteria</strong> (set in <code>gram_negative</code>) are:</p><ul><li><p>Cefotaxime</p></li>
<li><p>Ceftazidime</p></li>
<li><p>Colistin</p></li>
<li><p>Gentamicin</p></li>
<li><p>Meropenem</p></li>
<li><p>Tobramycin</p></li>
</ul><p>The default antimicrobial agents used for <strong>Gram-positive bacteria</strong> (set in <code>gram_positive</code>) are:</p><ul><li><p>Erythromycin</p></li>
<li><p>Oxacillin</p></li>
<li><p>Rifampin</p></li>
<li><p>Teicoplanin</p></li>
<li><p>Tetracycline</p></li>
<li><p>Vancomycin</p></li>
</ul><p>The default antimicrobial agents used for <strong>fungi</strong> (set in <code>antifungal</code>) are:</p><ul><li><p>Anidulafungin</p></li>
<li><p>Caspofungin</p></li>
<li><p>Fluconazole</p></li>
<li><p>Miconazole</p></li>
<li><p>Nystatin</p></li>
<li><p>Voriconazole</p></li>
</ul></div>
<div id="stable-lifecycle">
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><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, an argument will be deprecated and first continue to work, but will emit a 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>
</div>
<div id="read-more-on-our-website-">
<h2>Read more on Our Website!</h2>
<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 data 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>.</p>
</div>
<div id="see-also">
<h2>See also</h2>
<div class="dont-index"><p><code><a href="first_isolate.html">first_isolate()</a></code></p></div>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># `example_isolates` is a data set available in the AMR package.</span></span>
<span><span class="co"># See ?example_isolates.</span></span>
<span></span>
<span><span class="co"># output of the `key_antimicrobials()` function could be like this:</span></span>
<span><span class="va">strainA</span> <span class="op">&lt;-</span> <span class="st">"SSSRR.S.R..S"</span></span>
<span><span class="va">strainB</span> <span class="op">&lt;-</span> <span class="st">"SSSIRSSSRSSS"</span></span>
<span></span>
<span><span class="co"># those strings can be compared with:</span></span>
<span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span><span class="op">)</span></span>
<span><span class="co"># TRUE, because I is ignored (as well as missing values)</span></span>
<span></span>
<span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span>, ignore_I <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span><span class="co"># FALSE, because I is not ignored and so the 4th [character] differs</span></span>
<span></span>
<span><span class="co"># \donttest{</span></span>
<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="co"># set key antibiotics to a new variable</span></span>
<span> <span class="va">my_patients</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>keyab <span class="op">=</span> <span class="fu">key_antimicrobials</span><span class="op">(</span>antifungal <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># no need to define `x`</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span>
<span> <span class="co"># now calculate first isolates</span></span>
<span> first_regular <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="co"># and first WEIGHTED isolates</span></span>
<span> first_weighted <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="st">"keyab"</span><span class="op">)</span></span>
<span> <span class="op">)</span></span>
<span> </span>
<span> <span class="co"># Check the difference, in this data set it results in more isolates:</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="op">}</span></span>
<span><span class="co"># }</span></span></code></pre></div>
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