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@ -38,7 +38,7 @@
<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="">1.8.2.9098</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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">
@ -61,60 +61,65 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
Data Sets for Download / Own Use
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
Import Data From SPSS/SAS/Stata
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get taxonomy of a microorganism
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic drug
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral drug
Get Properties of an Antiviral Drug
</a>
</div>
</li>
@ -375,19 +380,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<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>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 I S R I S S</span></span>
<span><span class="co"># 2 I R R I S I</span></span>
<span><span class="co"># 3 I R S I R I</span></span>
<span><span class="co"># 4 S S I S R I</span></span>
<span><span class="co"># 5 I I R I I S</span></span>
<span><span class="co"># 6 R S S S R I</span></span>
<span><span class="co"># 1 I R R R S R</span></span>
<span><span class="co"># 2 R I R S R S</span></span>
<span><span class="co"># 3 R R R I I R</span></span>
<span><span class="co"># 4 I S R R S I</span></span>
<span><span class="co"># 5 S R R S R R</span></span>
<span><span class="co"># 6 S I R I S R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -428,40 +433,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3130</td>
<td align="right">62.60%</td>
<td align="right">3130</td>
<td align="right">62.60%</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1022</td>
<td align="right">20.44%</td>
<td align="right">4152</td>
<td align="right">83.04%</td>
<td align="right">976</td>
<td align="right">19.52%</td>
<td align="right">4203</td>
<td align="right">84.06%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">476</td>
<td align="right">9.52%</td>
<td align="right">4628</td>
<td align="right">92.56%</td>
<td align="right">442</td>
<td align="right">8.84%</td>
<td align="right">4645</td>
<td align="right">92.90%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">269</td>
<td align="right">5.38%</td>
<td align="right">4897</td>
<td align="right">97.94%</td>
<td align="right">247</td>
<td align="right">4.94%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">103</td>
<td align="right">2.06%</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>