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<meta property="og:description" content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables." />
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<h1>EUCAST rules</h1>
<div class="hidden name"><code>eucast_rules.Rd</code></div>
</div>
<div class="ref-description">
<p>Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href='http://eucast.org'>http://eucast.org</a>), see <em>Source</em>. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.</p>
</div>
<pre class="usage"><span class='fu'>eucast_rules</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>amcl</span> <span class='kw'>=</span> <span class='st'>"amcl"</span>, <span class='kw'>amik</span> <span class='kw'>=</span> <span class='st'>"amik"</span>, <span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"amox"</span>, <span class='kw'>ampi</span> <span class='kw'>=</span> <span class='st'>"ampi"</span>,
<span class='kw'>azit</span> <span class='kw'>=</span> <span class='st'>"azit"</span>, <span class='kw'>azlo</span> <span class='kw'>=</span> <span class='st'>"azlo"</span>, <span class='kw'>aztr</span> <span class='kw'>=</span> <span class='st'>"aztr"</span>, <span class='kw'>cefa</span> <span class='kw'>=</span> <span class='st'>"cefa"</span>,
<span class='kw'>cfep</span> <span class='kw'>=</span> <span class='st'>"cfep"</span>, <span class='kw'>cfot</span> <span class='kw'>=</span> <span class='st'>"cfot"</span>, <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='st'>"cfox"</span>, <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='st'>"cfra"</span>,
<span class='kw'>cfta</span> <span class='kw'>=</span> <span class='st'>"cfta"</span>, <span class='kw'>cftr</span> <span class='kw'>=</span> <span class='st'>"cftr"</span>, <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='st'>"cfur"</span>, <span class='kw'>chlo</span> <span class='kw'>=</span> <span class='st'>"chlo"</span>,
<span class='kw'>cipr</span> <span class='kw'>=</span> <span class='st'>"cipr"</span>, <span class='kw'>clar</span> <span class='kw'>=</span> <span class='st'>"clar"</span>, <span class='kw'>clin</span> <span class='kw'>=</span> <span class='st'>"clin"</span>, <span class='kw'>clox</span> <span class='kw'>=</span> <span class='st'>"clox"</span>,
<span class='kw'>coli</span> <span class='kw'>=</span> <span class='st'>"coli"</span>, <span class='kw'>czol</span> <span class='kw'>=</span> <span class='st'>"czol"</span>, <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='st'>"dapt"</span>, <span class='kw'>doxy</span> <span class='kw'>=</span> <span class='st'>"doxy"</span>,
<span class='kw'>erta</span> <span class='kw'>=</span> <span class='st'>"erta"</span>, <span class='kw'>eryt</span> <span class='kw'>=</span> <span class='st'>"eryt"</span>, <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='st'>"fosf"</span>, <span class='kw'>fusi</span> <span class='kw'>=</span> <span class='st'>"fusi"</span>,
<span class='kw'>gent</span> <span class='kw'>=</span> <span class='st'>"gent"</span>, <span class='kw'>imip</span> <span class='kw'>=</span> <span class='st'>"imip"</span>, <span class='kw'>kana</span> <span class='kw'>=</span> <span class='st'>"kana"</span>, <span class='kw'>levo</span> <span class='kw'>=</span> <span class='st'>"levo"</span>,
<span class='kw'>linc</span> <span class='kw'>=</span> <span class='st'>"linc"</span>, <span class='kw'>line</span> <span class='kw'>=</span> <span class='st'>"line"</span>, <span class='kw'>mero</span> <span class='kw'>=</span> <span class='st'>"mero"</span>, <span class='kw'>mezl</span> <span class='kw'>=</span> <span class='st'>"mezl"</span>,
<span class='kw'>mino</span> <span class='kw'>=</span> <span class='st'>"mino"</span>, <span class='kw'>moxi</span> <span class='kw'>=</span> <span class='st'>"moxi"</span>, <span class='kw'>nali</span> <span class='kw'>=</span> <span class='st'>"nali"</span>, <span class='kw'>neom</span> <span class='kw'>=</span> <span class='st'>"neom"</span>,
<span class='kw'>neti</span> <span class='kw'>=</span> <span class='st'>"neti"</span>, <span class='kw'>nitr</span> <span class='kw'>=</span> <span class='st'>"nitr"</span>, <span class='kw'>norf</span> <span class='kw'>=</span> <span class='st'>"norf"</span>, <span class='kw'>novo</span> <span class='kw'>=</span> <span class='st'>"novo"</span>,
<span class='kw'>oflo</span> <span class='kw'>=</span> <span class='st'>"oflo"</span>, <span class='kw'>oxac</span> <span class='kw'>=</span> <span class='st'>"oxac"</span>, <span class='kw'>peni</span> <span class='kw'>=</span> <span class='st'>"peni"</span>, <span class='kw'>pipe</span> <span class='kw'>=</span> <span class='st'>"pipe"</span>,
<span class='kw'>pita</span> <span class='kw'>=</span> <span class='st'>"pita"</span>, <span class='kw'>poly</span> <span class='kw'>=</span> <span class='st'>"poly"</span>, <span class='kw'>pris</span> <span class='kw'>=</span> <span class='st'>"pris"</span>, <span class='kw'>qida</span> <span class='kw'>=</span> <span class='st'>"qida"</span>,
<span class='kw'>rifa</span> <span class='kw'>=</span> <span class='st'>"rifa"</span>, <span class='kw'>roxi</span> <span class='kw'>=</span> <span class='st'>"roxi"</span>, <span class='kw'>siso</span> <span class='kw'>=</span> <span class='st'>"siso"</span>, <span class='kw'>teic</span> <span class='kw'>=</span> <span class='st'>"teic"</span>,
<span class='kw'>tetr</span> <span class='kw'>=</span> <span class='st'>"tetr"</span>, <span class='kw'>tica</span> <span class='kw'>=</span> <span class='st'>"tica"</span>, <span class='kw'>tige</span> <span class='kw'>=</span> <span class='st'>"tige"</span>, <span class='kw'>tobr</span> <span class='kw'>=</span> <span class='st'>"tobr"</span>,
<span class='kw'>trim</span> <span class='kw'>=</span> <span class='st'>"trim"</span>, <span class='kw'>trsu</span> <span class='kw'>=</span> <span class='st'>"trsu"</span>, <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='st'>"vanc"</span>)
<span class='fu'>EUCAST_rules</span>(<span class='no'>...</span>)
<span class='fu'>interpretive_reading</span>(<span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>tbl</th>
<td><p>table with antibiotic columns, like e.g. <code>amox</code> and <code>amcl</code></p></td>
</tr>
<tr>
<th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr>
<tr>
<th>info</th>
<td><p>print progress</p></td>
</tr>
<tr>
<th>rules</th>
<td><p>a character vector that specifies which rules should be applied - one or more of <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c("breakpoints", "expert", "other", "all")</a></code></p></td>
</tr>
<tr>
<th>verbose</th>
<td><p>a logical to indicate whether extensive info should be returned as a <code>data.frame</code> with info about which rows and columns are effected</p></td>
</tr>
<tr>
<th>amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc</th>
<td><p>column name of an antibiotic, see Antibiotics</p></td>
</tr>
<tr>
<th>...</th>
<td><p>parameters that are passed on to <code>eucast_rules</code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<ul>
<li><p>EUCAST Expert Rules. Version 2.0, 2012. <br />
Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60. <br />
<a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>https://doi.org/10.1111/j.1469-0691.2011.03703.x</a></p></li>
<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1, 2018. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx</a></p></li>
</ul>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The input of <code>tbl</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <code>data.frame</code> with verbose info.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
<p>To define antibiotics column names, input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
<p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p>
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<em>J01CR02</em>),
<strong>amik</strong>: amikacin (<em>J01GB06</em>),
<strong>amox</strong>: amoxicillin (<em>J01CA04</em>),
<strong>ampi</strong>: ampicillin (<em>J01CA01</em>),
<strong>azit</strong>: azithromycin (<em>J01FA10</em>),
<strong>azlo</strong>: azlocillin (<em>J01CA09</em>),
<strong>aztr</strong>: aztreonam (<em>J01DF01</em>),
<strong>cefa</strong>: cefaloridine (<em>J01DB02</em>),
<strong>cfep</strong>: cefepime (<em>J01DE01</em>),
<strong>cfot</strong>: cefotaxime (<em>J01DD01</em>),
<strong>cfox</strong>: cefoxitin (<em>J01DC01</em>),
<strong>cfra</strong>: cefradine (<em>J01DB09</em>),
<strong>cfta</strong>: ceftazidime (<em>J01DD02</em>),
<strong>cftr</strong>: ceftriaxone (<em>J01DD04</em>),
<strong>cfur</strong>: cefuroxime (<em>J01DC02</em>),
<strong>chlo</strong>: chloramphenicol (<em>J01BA01</em>),
<strong>cipr</strong>: ciprofloxacin (<em>J01MA02</em>),
<strong>clar</strong>: clarithromycin (<em>J01FA09</em>),
<strong>clin</strong>: clindamycin (<em>J01FF01</em>),
<strong>clox</strong>: flucloxacillin (<em>J01CF05</em>),
<strong>coli</strong>: colistin (<em>J01XB01</em>),
<strong>czol</strong>: cefazolin (<em>J01DB04</em>),
<strong>dapt</strong>: daptomycin (<em>J01XX09</em>),
<strong>doxy</strong>: doxycycline (<em>J01AA02</em>),
<strong>erta</strong>: ertapenem (<em>J01DH03</em>),
<strong>eryt</strong>: erythromycin (<em>J01FA01</em>),
<strong>fosf</strong>: fosfomycin (<em>J01XX01</em>),
<strong>fusi</strong>: fusidic acid (<em>J01XC01</em>),
<strong>gent</strong>: gentamicin (<em>J01GB03</em>),
<strong>imip</strong>: imipenem (<em>J01DH51</em>),
<strong>kana</strong>: kanamycin (<em>J01GB04</em>),
<strong>levo</strong>: levofloxacin (<em>J01MA12</em>),
<strong>linc</strong>: lincomycin (<em>J01FF02</em>),
<strong>line</strong>: linezolid (<em>J01XX08</em>),
<strong>mero</strong>: meropenem (<em>J01DH02</em>),
<strong>mezl</strong>: mezlocillin (<em>J01CA10</em>),
<strong>mino</strong>: minocycline (<em>J01AA08</em>),
<strong>moxi</strong>: moxifloxacin (<em>J01MA14</em>),
<strong>nali</strong>: nalidixic acid (<em>J01MB02</em>),
<strong>neom</strong>: neomycin (<em>J01GB05</em>),
<strong>neti</strong>: netilmicin (<em>J01GB07</em>),
<strong>nitr</strong>: nitrofurantoin (<em>J01XE01</em>),
<strong>norf</strong>: norfloxacin (<em>J01MA06</em>),
<strong>novo</strong>: novobiocin (an ATCvet code: <em>QJ01XX95</em>),
<strong>oflo</strong>: ofloxacin (<em>J01MA01</em>),
<strong>peni</strong>: penicillin (<em>J01RA01</em>),
<strong>pipe</strong>: piperacillin (<em>J01CA12</em>),
<strong>pita</strong>: piperacillin+tazobactam (<em>J01CR05</em>),
<strong>poly</strong>: polymyxin B (<em>J01XB02</em>),
<strong>pris</strong>: pristinamycin (<em>J01FG01</em>),
<strong>qida</strong>: quinupristin/dalfopristin (<em>J01FG02</em>),
<strong>rifa</strong>: rifampicin (<em>J04AB02</em>),
<strong>roxi</strong>: roxithromycin (<em>J01FA06</em>),
<strong>siso</strong>: sisomicin (<em>J01GB08</em>),
<strong>teic</strong>: teicoplanin (<em>J01XA02</em>),
<strong>tetr</strong>: tetracycline (<em>J01AA07</em>),
<strong>tica</strong>: ticarcillin (<em>J01CA13</em>),
<strong>tige</strong>: tigecycline (<em>J01AA12</em>),
<strong>tobr</strong>: tobramycin (<em>J01GB01</em>),
<strong>trim</strong>: trimethoprim (<em>J01EA01</em>),
<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<em>J01EE01</em>),
<strong>vanc</strong>: vancomycin (<em>J01XA01</em>).</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>septic_patients</span>)
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
<span class='st'>"Enterococcus faecalis"</span>,
<span class='st'>"Escherichia coli"</span>,
<span class='st'>"Klebsiella pneumoniae"</span>,
<span class='st'>"Pseudomonas aeruginosa"</span>),
<span class='kw'>vanc</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
<span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
<span class='kw'>coli</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Colistin</span>
<span class='kw'>cfta</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
<span class='kw'>cfur</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
<span class='kw'>peni</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Benzylpenicillin</span>
<span class='kw'>cfox</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='no'>a</span>
<span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
<span class='co'># 1 Staphylococcus aureus - - - - - S S</span>
<span class='co'># 2 Enterococcus faecalis - - - - - S S</span>
<span class='co'># 3 Escherichia coli - - - - - S S</span>
<span class='co'># 4 Klebsiella pneumoniae - - - - - S S</span>
<span class='co'># 5 Pseudomonas aeruginosa - - - - - S S</span>
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='st'>"mo"</span>) <span class='co'># 18 results are forced as R or S</span>
<span class='no'>b</span>
<span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
<span class='co'># 1 Staphylococcus aureus - S R R S S S</span>
<span class='co'># 2 Enterococcus faecalis - - R R R S R</span>
<span class='co'># 3 Escherichia coli R - - - - R S</span>
<span class='co'># 4 Klebsiella pneumoniae R R - - - R S</span>
<span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</span>
<span class='co'># }</span></pre>
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<li><a href="#arguments">Arguments</a></li>
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<li><a href="#value">Value</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
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