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@ -38,7 +38,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9022</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -226,7 +226,7 @@
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<span><span class="co"># 3. Otherwise: Negative</span></span>
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<span><span class="co"># </span></span>
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<span><span class="co"># Unmatched rows will return NA.</span></span>
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<span><span class="co"># Results will be of class <factor>, with ordered levels: Negative < Elderly Type A < Elderly Type B</span></span></code></pre></div>
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<span><span class="co"># Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < Elderly Type B</span></span></code></pre></div>
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<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code><a href="../reference/mdro.html">mdro()</a></code> function:</p>
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<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span></span>
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@ -314,19 +314,19 @@ Unique: 2</p>
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<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
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<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
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<span><span class="co"># 1 S I R R I R</span></span>
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<span><span class="co"># 2 I S R S R I</span></span>
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<span><span class="co"># 3 R I R I R S</span></span>
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<span><span class="co"># 4 S R I I R R</span></span>
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<span><span class="co"># 5 I I S S S R</span></span>
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<span><span class="co"># 6 R R S I I R</span></span>
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<span><span class="co"># 1 R S I S I S</span></span>
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<span><span class="co"># 2 R R I R R I</span></span>
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<span><span class="co"># 3 R I S I I I</span></span>
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<span><span class="co"># 4 R R S I S S</span></span>
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<span><span class="co"># 5 R R S R I R</span></span>
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<span><span class="co"># 6 S S R I S S</span></span>
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<span><span class="co"># kanamycin</span></span>
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<span><span class="co"># 1 S</span></span>
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<span><span class="co"># 1 R</span></span>
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<span><span class="co"># 2 S</span></span>
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<span><span class="co"># 3 R</span></span>
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<span><span class="co"># 4 R</span></span>
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<span><span class="co"># 4 I</span></span>
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<span><span class="co"># 5 S</span></span>
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<span><span class="co"># 6 R</span></span></code></pre></div>
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<span><span class="co"># 6 I</span></span></code></pre></div>
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<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
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<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
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@ -357,40 +357,40 @@ Unique: 5</p>
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<tr class="odd">
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<td align="left">1</td>
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<td align="left">Mono-resistant</td>
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<td align="right">3172</td>
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<td align="right">63.44%</td>
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<td align="right">3172</td>
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<td align="right">63.44%</td>
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<td align="right">3161</td>
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<td align="right">63.22%</td>
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<td align="right">3161</td>
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<td align="right">63.22%</td>
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</tr>
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<tr class="even">
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<td align="left">2</td>
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<td align="left">Negative</td>
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<td align="right">973</td>
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<td align="right">19.46%</td>
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<td align="right">4145</td>
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<td align="right">82.90%</td>
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<td align="right">1035</td>
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<td align="right">20.70%</td>
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<td align="right">4196</td>
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<td align="right">83.92%</td>
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</tr>
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<tr class="odd">
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<td align="left">3</td>
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<td align="left">Multi-drug-resistant</td>
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<td align="right">489</td>
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<td align="right">9.78%</td>
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<td align="right">4634</td>
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<td align="right">92.68%</td>
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<td align="right">452</td>
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<td align="right">9.04%</td>
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<td align="right">4648</td>
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<td align="right">92.96%</td>
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</tr>
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<tr class="even">
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<td align="left">4</td>
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<td align="left">Poly-resistant</td>
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<td align="right">247</td>
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<td align="right">4.94%</td>
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<td align="right">4881</td>
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<td align="right">97.62%</td>
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<td align="right">241</td>
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<td align="right">4.82%</td>
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<td align="right">4889</td>
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<td align="right">97.78%</td>
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</tr>
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<tr class="odd">
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<td align="left">5</td>
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<td align="left">Extensively drug-resistant</td>
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<td align="right">119</td>
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<td align="right">2.38%</td>
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<td align="right">111</td>
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<td align="right">2.22%</td>
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<td align="right">5000</td>
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<td align="right">100.00%</td>
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</tr>
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