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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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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="">2.1.1.9183</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</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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@@ -84,7 +84,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
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<dd><p>a data set with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
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<dd><p>a data set with antimicrobials columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
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<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
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@@ -116,7 +116,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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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 antibiotic 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 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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<dt id="arg-custom-rules">custom_rules<a class="anchor" aria-label="anchor" href="#arg-custom-rules"></a></dt>
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@@ -128,11 +128,11 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
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<dd><p>column name of an antibiotic, see section <em>Antibiotics</em> below</p></dd>
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<dd><p>column name of an antimicrobial, see section <em>Antimicrobials</em> below</p></dd>
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<dt id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></dt>
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<dd><p>any (vector of) text that can be coerced to a valid antibiotic drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
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<dd><p>any (vector of) text that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
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<dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt>
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@@ -141,7 +141,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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</dl></div>
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<div class="section level2">
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<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
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<p>The input of <code>x</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with all original and new values of the affected bug-drug combinations.</p>
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<p>The input of <code>x</code>, possibly with edited values of antimicrobials. Or, if <code>verbose = TRUE</code>, a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with all original and new values of the affected bug-drug combinations.</p>
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</div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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@@ -169,18 +169,18 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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</div>
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<div class="section level2">
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<h2 id="antibiotics">Antibiotics<a class="anchor" aria-label="anchor" href="#antibiotics"></a></h2>
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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 antibiotics 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 antibiotics are eligible for the functions <code>eucast_rules()</code> and <code><a href="mdro.html">mdro()</a></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>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>eucast_rules()</code> and <code><a href="mdro.html">mdro()</a></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>), 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>), 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/atc_ddd_index//?code=S01AE08&showdescription=no" class="external-link">S01AE08</a>), biapenem (<code>BIA</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no" class="external-link">J01DH05</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_index//?code=J01DB03&showdescription=no" class="external-link">J01DB03</a>), cefamandole (<code>MAN</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DC03&showdescription=no" class="external-link">J01DC03</a>), cefapirin (<code>HAP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB08&showdescription=no" class="external-link">J01DB08</a>), cefatrizine (<code>CTZ</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB07&showdescription=no" class="external-link">J01DB07</a>), cefazedone (<code>CZD</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB06&showdescription=no" class="external-link">J01DB06</a>), cefazolin (<code>CZO</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB04&showdescriptLine truncated
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</div>
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<div class="section level2">
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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<p>All data sets in this <code>AMR</code> package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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</div>
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<div class="section level2">
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