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(v1.4.0.9044) mo tibble printing, mo_shortname() fix
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<title>How to determine multi-drug resistance (MDR) • AMR (for R)</title>
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@ -56,7 +39,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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@ -268,7 +251,7 @@
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<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%>%</span>
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<span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%>%</span>
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span>
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<span class="co"># Warning in warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ", : NA introduced for isolates where the available percentage of antimicrobial</span>
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<span class="co"># Warning: NA introduced for isolates where the available percentage of antimicrobial</span>
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<span class="co"># classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
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<p><strong>Frequency table</strong></p>
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<p>Class: factor > ordered (numeric)<br>
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@ -306,48 +289,41 @@ Unique: 2</p>
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</table>
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<p>For another example, I will create a data set to determine multi-drug resistant TB:</p>
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<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span class="co"># a helper function to get a random vector with values S, I and R</span>
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<span class="co"># with the probabilities 50% - 10% - 40%</span>
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<span class="va">sample_rsi</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="op">)</span> <span class="op">{</span>
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<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span><span class="op">)</span>,
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size <span class="op">=</span> <span class="fl">5000</span>,
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prob <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span><span class="op">)</span>,
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replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
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<span class="op">}</span>
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<span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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isoniazid <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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gatifloxacin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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ethambutol <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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pyrazinamide <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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moxifloxacin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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kanamycin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
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<code class="sourceCode R"><span class="co"># random_rsi() is a helper function to generate</span>
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<span class="co"># a random vector with values S, I and R</span>
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<span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
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<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
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<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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INH <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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GAT <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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ETH <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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PZA <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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MFX <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
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KAN <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
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<code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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PZA <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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MFX <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
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KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
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<p>The data set now looks like this:</p>
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<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
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<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
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<span class="co"># 1 S R S R R S</span>
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<span class="co"># 2 S R S S S S</span>
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<span class="co"># 3 S S S S R S</span>
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<span class="co"># 4 S R S R S S</span>
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<span class="co"># 5 R S R S R S</span>
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<span class="co"># 6 S R R R S S</span>
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<span class="co"># 1 S S R I R S</span>
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<span class="co"># 2 I S R I I R</span>
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<span class="co"># 3 R R R S I R</span>
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<span class="co"># 4 I I R R S S</span>
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<span class="co"># 5 I R I S S R</span>
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<span class="co"># 6 I R I I S I</span>
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<span class="co"># kanamycin</span>
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<span class="co"># 1 S</span>
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<span class="co"># 1 R</span>
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<span class="co"># 2 S</span>
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<span class="co"># 3 S</span>
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<span class="co"># 4 S</span>
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<span class="co"># 5 R</span>
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<span class="co"># 6 S</span></code></pre></div>
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<span class="co"># 3 I</span>
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<span class="co"># 4 I</span>
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<span class="co"># 5 I</span>
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<span class="co"># 6 R</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="cb6"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><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></code></pre></div>
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@ -378,40 +354,40 @@ 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">3314</td>
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<td align="right">66.28%</td>
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<td align="right">3314</td>
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<td align="right">66.28%</td>
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<td align="right">3214</td>
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<td align="right">64.28%</td>
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<td align="right">3214</td>
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<td align="right">64.28%</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">637</td>
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<td align="right">12.74%</td>
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<td align="right">3951</td>
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<td align="right">79.02%</td>
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<td align="right">997</td>
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<td align="right">19.94%</td>
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<td align="right">4211</td>
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<td align="right">84.22%</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">565</td>
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<td align="right">11.30%</td>
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<td align="right">4516</td>
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<td align="right">90.32%</td>
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<td align="right">442</td>
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<td align="right">8.84%</td>
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<td align="right">4653</td>
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<td align="right">93.06%</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">298</td>
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<td align="right">5.96%</td>
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<td align="right">4814</td>
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<td align="right">96.28%</td>
|
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<td align="right">239</td>
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<td align="right">4.78%</td>
|
||||
<td align="right">4892</td>
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<td align="right">97.84%</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">186</td>
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<td align="right">3.72%</td>
|
||||
<td align="right">108</td>
|
||||
<td align="right">2.16%</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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@ -433,7 +409,7 @@ Unique: 5</p>
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</div>
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<div class="pkgdown">
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<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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