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(v1.4.0.9032) auto-data guessing for functions
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@ -39,7 +39,7 @@
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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">1.4.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
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</span>
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</div>
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@ -217,7 +217,11 @@
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<p>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>)</p>
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</li>
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<li>
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<p><code>guideline = "EUCAST"</code></p>
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<p><code>guideline = "EUCAST3.2"</code> (or simply <code>guideline = "EUCAST"</code>)</p>
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<p>The European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance and Unusual Phenotypes” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf">link</a>)</p>
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</li>
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<li>
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<p><code>guideline = "EUCAST3.1"</code></p>
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<p>The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf">link</a>)</p>
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</li>
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<li>
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@ -226,13 +230,14 @@
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</li>
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<li>
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<p><code>guideline = "MRGN"</code></p>
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<p>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>)</p>
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<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p>
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</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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<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (<a href="https://www.rivm.nl/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>Please suggest your own (country-specific) guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="uri">https://github.com/msberends/AMR/issues/new</a>.</p>
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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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@ -246,8 +251,8 @@
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<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 mdro(.): NA introduced for isolates where the available percentage of</span>
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<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></pre></div>
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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"># classes was below 50% (set with `pct_required_classes`)</span></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<br>
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@ -313,26 +318,27 @@ Unique: 2</p>
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<div class="sourceCode" id="cb5"><pre class="downlit">
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<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 R S S R R S</span>
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<span class="co"># 2 I R S R S I</span>
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<span class="co"># 3 R R S S S S</span>
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<span class="co"># 4 R R S I S S</span>
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<span class="co"># 5 S I R S R S</span>
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<span class="co"># 6 S S S R S S</span>
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<span class="co"># 1 S I R S R R</span>
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<span class="co"># 2 R S S R I S</span>
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<span class="co"># 3 I R I S R S</span>
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<span class="co"># 4 I S S R S R</span>
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<span class="co"># 5 R R S S R R</span>
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<span class="co"># 6 S R I S 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 S</span>
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<span class="co"># 6 R</span></pre></div>
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<span class="co"># 4 R</span>
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<span class="co"># 5 R</span>
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<span class="co"># 6 S</span></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">
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<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></pre></div>
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<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
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<div class="sourceCode" id="cb7"><pre class="downlit">
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<span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
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<span class="co"># NOTE: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></pre></div>
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<span class="co"># NOTE: No column found as input for `col_mo`, assuming all records contain</span>
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<span class="co"># Mycobacterium tuberculosis.</span></pre></div>
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<p>Create a frequency table of the results:</p>
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<div class="sourceCode" id="cb8"><pre class="downlit">
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></pre></div>
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@ -355,40 +361,40 @@ 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">3262</td>
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<td align="right">65.24%</td>
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<td align="right">3262</td>
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<td align="right">65.24%</td>
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<td align="right">3313</td>
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<td align="right">66.26%</td>
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<td align="right">3313</td>
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<td align="right">66.26%</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">664</td>
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<td align="right">13.28%</td>
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<td align="right">3926</td>
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<td align="right">78.52%</td>
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<td align="right">631</td>
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<td align="right">12.62%</td>
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<td align="right">3944</td>
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<td align="right">78.88%</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">609</td>
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<td align="right">12.18%</td>
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<td align="right">4535</td>
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<td align="right">90.70%</td>
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<td align="right">575</td>
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<td align="right">11.50%</td>
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<td align="right">4519</td>
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<td align="right">90.38%</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">283</td>
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<td align="right">5.66%</td>
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<td align="right">4818</td>
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<td align="right">96.36%</td>
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<td align="right">275</td>
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<td align="right">5.50%</td>
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<td align="right">4794</td>
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<td align="right">95.88%</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">182</td>
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<td align="right">3.64%</td>
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<td align="right">206</td>
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<td align="right">4.12%</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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