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(v0.8.0.9021) update vignettes
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@ -41,7 +41,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9021</span>
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</span>
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</div>
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<h1>How to determine multi-drug resistance (MDR)</h1>
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<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">16 October 2019</h4>
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<h4 class="date">09 November 2019</h4>
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<div class="hidden name"><code>MDR.Rmd</code></div>
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@ -196,67 +196,148 @@
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<p>With the function <code><a href="../reference/mdro.html">mdro()</a></code>, you can determine multi-drug resistant organisms (MDRO). It currently support these guidelines:</p>
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<p>With the function <code><a href="../reference/mdro.html">mdro()</a></code>, you can determine multi-drug resistant organisms (MDRO).</p>
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<div id="type-of-input" class="section level4">
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<h4 class="hasAnchor">
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<a href="#type-of-input" class="anchor"></a>Type of input</h4>
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<p>The <code><a href="../reference/mdro.html">mdro()</a></code> takes a data set as input, such as a regular <code>data.frame</code>. It automatically determines the right columns for info about your isolates, like the name of the species and all columns with results of antimicrobial agents. See the help page for more info about how to set the right settings for your data with the command <code><a href="../reference/mdro.html">?mdro</a></code>.</p>
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<p>For WHONET data (and most other data), all settings are automatically set correctly.</p>
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</div>
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<div id="guidelines" class="section level4">
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<h4 class="hasAnchor">
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<a href="#guidelines" class="anchor"></a>Guidelines</h4>
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<p>The function support multiple guidelines. You can select a guideline with the <code>guideline</code> parameter. Currently supported guidelines are (case-insensitive):</p>
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<ul>
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<li>“Intrinsic Resistance and Exceptional Phenotypes Tables”, by EUCAST (European Committee on Antimicrobial Susceptibility Testing)</li>
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<li>“Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis”, by WHO (World Health Organization)</li>
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<li>“WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)”, by RIVM (Rijksinstituut voor de Volksgezondheid, the Netherlands National Institute for Public Health and the Environment)</li>
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<li>
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<p><code>guideline = "CMI2012"</code> (default)</p>
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Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext">link</a>)</li>
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<li>
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<p><code>guideline = "EUCAST"</code></p>
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The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf">link</a>)</li>
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<li>
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<p><code>guideline = "TB"</code></p>
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The international guideline for multi-drug resistant tuberculosis - World Health Organization “Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis” (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/">link</a>)</li>
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<li>
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<p><code>guideline = "MRGN"</code></p>
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The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. (<a href="https://doi.org/10.1186/s13756-015-0047-6">link</a>)</li>
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<li>
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<p><code>guideline = "BRMO"</code></p>
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<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]” (<a href="https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH">link</a>)</p>
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</li>
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</ul>
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<p>As an example, I will make a data set to determine multi-drug resistant TB:</p>
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="co"># a helper function to get a random vector with values S, I and R</span></a>
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<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co"># with the probabilities 50% - 10% - 40%</span></a>
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<a class="sourceLine" id="cb1-3" data-line-number="3">sample_rsi <-<span class="st"> </span><span class="cf">function</span>() {</a>
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<a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</a>
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<a class="sourceLine" id="cb1-5" data-line-number="5"> <span class="dt">size =</span> <span class="dv">5000</span>,</a>
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<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),</a>
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<a class="sourceLine" id="cb1-7" data-line-number="7"> <span class="dt">replace =</span> <span class="ot">TRUE</span>)</a>
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<a class="sourceLine" id="cb1-8" data-line-number="8">}</a>
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<a class="sourceLine" id="cb1-9" data-line-number="9"></a>
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<a class="sourceLine" id="cb1-10" data-line-number="10">my_TB_data <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">rifampicin =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb1-11" data-line-number="11"> <span class="dt">isoniazid =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb1-12" data-line-number="12"> <span class="dt">gatifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb1-13" data-line-number="13"> <span class="dt">ethambutol =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb1-14" data-line-number="14"> <span class="dt">pyrazinamide =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb1-15" data-line-number="15"> <span class="dt">moxifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb1-16" data-line-number="16"> <span class="dt">kanamycin =</span> <span class="kw">sample_rsi</span>())</a></code></pre></div>
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</div>
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<div id="examples" class="section level4">
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<h4 class="hasAnchor">
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<a href="#examples" class="anchor"></a>Examples</h4>
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<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code>. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order. If we test that guideline on the included <code>example_isolates</code> data set, we get:</p>
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr) <span class="co"># to support pipes: %>%</span></a></code></pre></div>
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<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">example_isolates <span class="op">%>%</span><span class="st"> </span></a>
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<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdro</a></span>() <span class="op">%>%</span><span class="st"> </span></a>
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<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>() <span class="co"># show frequency table of the result</span></a>
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<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
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<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Auto-guessing columns suitable for analysis...OK.</span></a>
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<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability will be improved if these antimicrobial results would be available too: SAM (ampicillin/sulbactam), ATM (aztreonam), CTT (cefotetan), CPT (ceftaroline), DAP (daptomycin), DOR (doripenem), ETP (ertapenem), FUS (fusidic acid), GEH (gentamicin-high), LVX (levofloxacin), MNO (minocycline), NET (netilmicin), PLB (polymyxin B), QDA (quinupristin/dalfopristin), STH (streptomycin-high), TLV (telavancin), TCC (ticarcillin/clavulanic acid)</span></a>
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<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co"># Table 1 - S. aureus ... OK</span></a>
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<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="co"># Table 2 - Enterococcus spp. ... OK</span></a>
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<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="co"># Table 3 - Enterobacteriaceae ... OK</span></a>
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<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># Table 4 - Pseudomonas aeruginosa ... OK</span></a>
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<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co"># Table 5 - Acinetobacter spp. ... OK</span></a>
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<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># Warning in mdro(.): NA introduced for isolates where the available</span></a>
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<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co"># percentage of antimicrobial classes was below 50% (set with</span></a>
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<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="co"># `pct_required_classes`)</span></a></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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Length: 2,000 (of which NA: 289 = 14.45%)<br>
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Levels: 4: Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant …<br>
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Unique: 2</p>
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<table class="table">
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<thead><tr class="header">
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<th align="left"></th>
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<th align="left">Item</th>
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<th align="right">Count</th>
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<th align="right">Percent</th>
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<th align="right">Cum. Count</th>
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<th align="right">Cum. Percent</th>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td align="left">1</td>
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<td align="left">Negative</td>
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<td align="right">1596</td>
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<td align="right">93.28%</td>
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<td align="right">1596</td>
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<td align="right">93.28%</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">Multi-drug-resistant (MDR)</td>
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<td align="right">115</td>
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<td align="right">6.72%</td>
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<td align="right">1711</td>
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<td align="right">100.00%</td>
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</tr>
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</tbody>
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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="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># a helper function to get a random vector with values S, I and R</span></a>
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||||
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># with the probabilities 50% - 10% - 40%</span></a>
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<a class="sourceLine" id="cb3-3" data-line-number="3">sample_rsi <-<span class="st"> </span><span class="cf">function</span>() {</a>
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<a class="sourceLine" id="cb3-4" data-line-number="4"> <span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</a>
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<a class="sourceLine" id="cb3-5" data-line-number="5"> <span class="dt">size =</span> <span class="dv">5000</span>,</a>
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<a class="sourceLine" id="cb3-6" data-line-number="6"> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),</a>
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<a class="sourceLine" id="cb3-7" data-line-number="7"> <span class="dt">replace =</span> <span class="ot">TRUE</span>)</a>
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<a class="sourceLine" id="cb3-8" data-line-number="8">}</a>
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<a class="sourceLine" id="cb3-9" data-line-number="9"></a>
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<a class="sourceLine" id="cb3-10" data-line-number="10">my_TB_data <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">rifampicin =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb3-11" data-line-number="11"> <span class="dt">isoniazid =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb3-12" data-line-number="12"> <span class="dt">gatifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb3-13" data-line-number="13"> <span class="dt">ethambutol =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb3-14" data-line-number="14"> <span class="dt">pyrazinamide =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb3-15" data-line-number="15"> <span class="dt">moxifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb3-16" data-line-number="16"> <span class="dt">kanamycin =</span> <span class="kw">sample_rsi</span>())</a></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="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">my_TB_data <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">RIF =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="dt">INH =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb2-3" data-line-number="3"> <span class="dt">GAT =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb2-4" data-line-number="4"> <span class="dt">ETH =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb2-5" data-line-number="5"> <span class="dt">PZA =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb2-6" data-line-number="6"> <span class="dt">MFX =</span> <span class="kw">sample_rsi</span>(),</a>
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<a class="sourceLine" id="cb2-7" data-line-number="7"> <span class="dt">KAN =</span> <span class="kw">sample_rsi</span>())</a></code></pre></div>
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<p>The data set looks like this now:</p>
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<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(my_TB_data)</a>
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<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
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<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 S S R S R S</span></a>
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||||
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 S R R S S R</span></a>
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<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 R R S S R S</span></a>
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<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 R R R S S S</span></a>
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||||
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 R R R R R R</span></a>
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||||
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 R R R I S R</span></a>
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<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># kanamycin</span></a>
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||||
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 I</span></a>
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||||
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 S</span></a>
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||||
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 R</span></a>
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||||
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 S</span></a>
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||||
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 R</span></a>
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||||
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># 6 S</span></a></code></pre></div>
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<p>We can now add the interpretation of MDR-TB to our data set:</p>
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<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">my_TB_data<span class="op">$</span>mdr <-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
|
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<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
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<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="co"># Determining multidrug-resistant organisms (MDRO), according to:</span></a>
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<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># Guideline: Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis</span></a>
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||||
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="co"># Version: WHO/HTM/TB/2014.11</span></a>
|
||||
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co"># Author: WHO (World Health Organization)</span></a>
|
||||
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
|
||||
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Auto-guessing columns suitable for analysis...</span></a>
|
||||
<a class="sourceLine" id="cb4-9" data-line-number="9"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability might be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></a></code></pre></div>
|
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<p>We also created a package dedicated to data cleaning and checking, called the <code>clean</code> package. It gets automatically installed with the <code>AMR</code> package, so we only have to load it:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(clean)</a></code></pre></div>
|
||||
<p>It contains the <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> function, to create a frequency table:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">my_TB_data <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">RIF =</span> <span class="kw">sample_rsi</span>(),</a>
|
||||
<a class="sourceLine" id="cb4-2" data-line-number="2"> <span class="dt">INH =</span> <span class="kw">sample_rsi</span>(),</a>
|
||||
<a class="sourceLine" id="cb4-3" data-line-number="3"> <span class="dt">GAT =</span> <span class="kw">sample_rsi</span>(),</a>
|
||||
<a class="sourceLine" id="cb4-4" data-line-number="4"> <span class="dt">ETH =</span> <span class="kw">sample_rsi</span>(),</a>
|
||||
<a class="sourceLine" id="cb4-5" data-line-number="5"> <span class="dt">PZA =</span> <span class="kw">sample_rsi</span>(),</a>
|
||||
<a class="sourceLine" id="cb4-6" data-line-number="6"> <span class="dt">MFX =</span> <span class="kw">sample_rsi</span>(),</a>
|
||||
<a class="sourceLine" id="cb4-7" data-line-number="7"> <span class="dt">KAN =</span> <span class="kw">sample_rsi</span>())</a></code></pre></div>
|
||||
<p>The data set now looks like this:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(my_TB_data)</a>
|
||||
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
|
||||
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># 1 S S R R S R</span></a>
|
||||
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># 2 S R S S R S</span></a>
|
||||
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="co"># 3 R S R S R R</span></a>
|
||||
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># 4 S S R S S I</span></a>
|
||||
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># 5 R R S R S S</span></a>
|
||||
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># 6 S S R R R S</span></a>
|
||||
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># kanamycin</span></a>
|
||||
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># 1 S</span></a>
|
||||
<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="co"># 2 S</span></a>
|
||||
<a class="sourceLine" id="cb5-12" data-line-number="12"><span class="co"># 3 R</span></a>
|
||||
<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co"># 4 R</span></a>
|
||||
<a class="sourceLine" id="cb5-14" data-line-number="14"><span class="co"># 5 S</span></a>
|
||||
<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># 6 R</span></a></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="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="../reference/mdro.html">mdro</a></span>(my_TB_data, <span class="dt">guideline =</span> <span class="st">"TB"</span>)</a></code></pre></div>
|
||||
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">my_TB_data<span class="op">$</span>mdr <-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
|
||||
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
|
||||
<a class="sourceLine" id="cb7-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Auto-guessing columns suitable for analysis...OK.</span></a>
|
||||
<a class="sourceLine" id="cb7-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability will be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></a>
|
||||
<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="co"># </span></a>
|
||||
<a class="sourceLine" id="cb7-6" data-line-number="6"><span class="co"># Only results with 'R' are considered as resistance. Use `combine_SI = FALSE` to also consider 'I' as resistance.</span></a>
|
||||
<a class="sourceLine" id="cb7-7" data-line-number="7"><span class="co"># </span></a>
|
||||
<a class="sourceLine" id="cb7-8" data-line-number="8"><span class="co"># Determining multidrug-resistant organisms (MDRO), according to:</span></a>
|
||||
<a class="sourceLine" id="cb7-9" data-line-number="9"><span class="co"># Guideline: Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis</span></a>
|
||||
<a class="sourceLine" id="cb7-10" data-line-number="10"><span class="co"># Version: WHO/HTM/TB/2014.11</span></a>
|
||||
<a class="sourceLine" id="cb7-11" data-line-number="11"><span class="co"># Author: WHO (World Health Organization)</span></a>
|
||||
<a class="sourceLine" id="cb7-12" data-line-number="12"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
|
||||
<a class="sourceLine" id="cb7-13" data-line-number="13"><span class="co"># </span></a>
|
||||
<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># => Found 4371 MDROs out of 5000 tested isolates (87.4%)</span></a></code></pre></div>
|
||||
<p>Create a frequency table of the results:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: factor > ordered (numeric)<br>
|
||||
Length: 5,000 (of which NA: 0 = 0%)<br>
|
||||
@ -275,46 +356,47 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3276</td>
|
||||
<td align="right">65.52%</td>
|
||||
<td align="right">3276</td>
|
||||
<td align="right">65.52%</td>
|
||||
<td align="right">3301</td>
|
||||
<td align="right">66.02%</td>
|
||||
<td align="right">3301</td>
|
||||
<td align="right">66.02%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">658</td>
|
||||
<td align="right">13.16%</td>
|
||||
<td align="right">3934</td>
|
||||
<td align="right">78.68%</td>
|
||||
<td align="right">629</td>
|
||||
<td align="right">12.58%</td>
|
||||
<td align="right">3930</td>
|
||||
<td align="right">78.60%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">616</td>
|
||||
<td align="right">12.32%</td>
|
||||
<td align="right">4550</td>
|
||||
<td align="right">91.00%</td>
|
||||
<td align="right">596</td>
|
||||
<td align="right">11.92%</td>
|
||||
<td align="right">4526</td>
|
||||
<td align="right">90.52%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">256</td>
|
||||
<td align="right">5.12%</td>
|
||||
<td align="right">4806</td>
|
||||
<td align="right">96.12%</td>
|
||||
<td align="right">282</td>
|
||||
<td align="right">5.64%</td>
|
||||
<td align="right">4808</td>
|
||||
<td align="right">96.16%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensive drug-resistant</td>
|
||||
<td align="right">194</td>
|
||||
<td align="right">3.88%</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">192</td>
|
||||
<td align="right">3.84%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
|
||||
|
||||
Reference in New Issue
Block a user