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@@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -58,19 +58,20 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mdro</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, guideline <span class="op">=</span> <span class="st">"CMI2012"</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, esbl <span class="op">=</span> <span class="cn">NA</span>,</span>
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<span> carbapenemase <span class="op">=</span> <span class="cn">NA</span>, mecA <span class="op">=</span> <span class="cn">NA</span>, mecC <span class="op">=</span> <span class="cn">NA</span>, vanA <span class="op">=</span> <span class="cn">NA</span>, vanB <span class="op">=</span> <span class="cn">NA</span>,</span>
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<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, pct_required_classes <span class="op">=</span> <span class="fl">0.5</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">custom_mdro_guideline</span><span class="op">(</span><span class="va">...</span>, as_factor <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">brmo</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span><span class="fu">brmo</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">mrgn</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span><span class="fu">mrgn</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">mdr_tb</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span><span class="fu">mdr_tb</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">mdr_cmi2012</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span><span class="fu">mdr_cmi2012</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">eucast_exceptional_phenotypes</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span><span class="fu">eucast_exceptional_phenotypes</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
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</div>
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@@ -135,7 +136,7 @@
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<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
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<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>).</p></dd>
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<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be included that were transformed to class <a href="as.sir.html">sir</a> on beforehand. Defaults to <code>FALSE</code> if no columns of <code>x</code> have a class <a href="as.sir.html">sir</a>.</p></dd>
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<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
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@@ -228,9 +229,8 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
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<h2 id="antimicrobials">Antimicrobials<a class="anchor" aria-label="anchor" href="#antimicrobials"></a></h2>
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<p>To define antimicrobials column names, leave as it is to determine it automatically with <code><a href="guess_ab_col.html">guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
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<p>The following antimicrobials are eligible for the functions <code><a href="eucast_rules.html">eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href="https://atcddd.fhi.no/atc/structure_and_principles/" class="external-link">ATC code</a>)', sorted alphabetically:</p>
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<p>Amikacin (<code>AMK</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&showdescription=no" class="external-link">J01GB06</a>), amoxicillin (<code>AMX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no" class="external-link">J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no" class="external-link">J01CR02</a>), amoxicillin/sulbactam (<code>AXS</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no" class="external-link">J01CR02</a>), ampicillin (<code>AMP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&showdescription=no" class="external-link">J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&showdescription=no" class="external-link">J01CR01</a>), apramycin (<code>APR</code>, <a href="https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no" class="external-link">QA07AA92</a>), arbekacin (<code>ARB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&showdescription=no" class="external-link">J01GB12</a>), aspoxicillin (<code>APX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&showdescription=no" class="external-link">J01CA19</a>), azidocillin (<code>AZD</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&showdescription=no" class="external-link">J01CE04</a>), azithromycin (<code>AZM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&showdescription=no" class="external-link">J01FA10</a>), azlocillin (<code>AZL</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&showdescription=no" class="external-link">J01CA09</a>), aztreonam (<code>ATM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&showdescription=no" class="external-link">J01DF01</a>), aztreonam/avibactam (<code>AZA</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&showdescription=no" class="external-link">J01DF51</a>), aztreonam/nacubactam (<code>ANC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&showdescription=no" class="external-link">J01DF51</a>), bacampicillin (<code>BAM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&showdescription=no" class="external-link">J01CA06</a>), bekanamycin (<code>BEK</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&showdescription=no" class="external-link">J01GB13</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&showdescription=no" class="external-link">J01CE08</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&showdescription=no" class="external-link">J01CE10</a>), benzylpenicillin (<code>PEN</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&showdescription=no" class="external-link">J01CE01</a>), besifloxacin (<code>BES</code>, <a href="https://atcddd.fhi.no/atcvet/atcvet_index/?code=QS01AE08&showdescription=no" class="external-link">QS01AE08</a>), biapenem (<code>BIA</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no" class="external-link">J01DH05</a>), bleomycin (<code>BLM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=L01DC01&showdescription=no" class="external-link">L01DC01</a>), brodimoprim (<code>BDP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01EA02&showdescription=no" class="external-link">J01EA02</a>), carbenicillin (<code>CRB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&showdescription=no" class="external-link">J01CA03</a>), carindacillin (<code>CRN</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&showdescription=no" class="external-link">J01CA05</a>), carumonam (<code>CAR</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&showdescription=no" class="external-link">J01DF02</a>), cefacetrile (<code>CAC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&showdescription=no" class="external-link">J01DB10</a>), cefaclor (<code>CEC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&showdescription=no" class="external-link">J01DC04</a>), cefadroxil (<code>CFR</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&showdescription=no" class="external-link">J01DB05</a>), cefalexin (<code>LEX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&showdescription=no" class="external-link">J01DB01</a>), cefaloridine (<code>RID</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&showdescription=no" class="external-link">J01DB02</a>), cefalotin (<code>CEP</code>, <a href="https://atcddd.fhi.no/atc_ddd_Line truncated
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<p>To let the function automatically detect antimicrobial column names, do not provide any named arguments. It will then use <code><a href="guess_ab_col.html">guess_ab_col()</a></code> to find them.</p>
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<p>To manually specify a column, provide its name (case-insensitive) as an argument, e.g. <code>AMX = "amoxicillin"</code>. To skip a specific antimicrobial, set it to <code>NULL</code>, e.g. <code>TIC = NULL</code> to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.</p>
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</div>
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<div class="section level2">
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<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
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