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@ -10,7 +10,7 @@
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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="">1.8.2.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9033</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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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>An object of class <code>rsi</code> (inherits from <code>ordered</code>, <code>factor</code>) of length 1.</p>
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</div>
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<div class="section level2">
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<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
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<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2013-2022, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
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<li><p><strong>M100 Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2013-2022, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
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<li><p><strong>Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2013-2022, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dt>guideline</dt>
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<dd><p>defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the <a href="rsi_translation.html">rsi_translation</a> data set), supports EUCAST (2011-2022) and CLSI (2011-2022), see <em>Details</em></p></dd>
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<dd><p>defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the <a href="rsi_translation.html">rsi_translation</a> data set), supports EUCAST (2013-2022) and CLSI (2013-2022), see <em>Details</em></p></dd>
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<dt>uti</dt>
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@ -268,7 +274,7 @@
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<h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
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<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022).</p>
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<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022).</p>
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<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2022"</code> or <code>"CLSI 2022"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
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</div>
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<h3 id="machine-readable-interpretation-guidelines">Machine-Readable Interpretation Guidelines<a class="anchor" aria-label="anchor" href="#machine-readable-interpretation-guidelines"></a></h3>
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<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 20,369 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
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<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 18,308 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
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</div>
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<div class="section">
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@ -484,16 +490,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2022-10-22 <span style="color: #949494;">08:23:30</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2022-10-22 <span style="color: #949494;">08:23:30</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2022-10-22 <span style="color: #949494;">08:23:31</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2022-10-22 <span style="color: #949494;">08:23:31</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2022-10-22 <span style="color: #949494;">08:23:31</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2022-10-22 <span style="color: #949494;">08:23:31</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2022-10-22 <span style="color: #949494;">08:23:32</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2022-10-22 <span style="color: #949494;">08:23:32</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2022-10-22 <span style="color: #949494;">08:23:32</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2022-10-22 <span style="color: #949494;">08:23:32</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2022-10-22 <span style="color: #949494;">20:06:45</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2022-10-22 <span style="color: #949494;">20:06:46</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2022-10-22 <span style="color: #949494;">20:06:46</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2022-10-22 <span style="color: #949494;">20:06:46</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2022-10-22 <span style="color: #949494;">20:06:46</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2022-10-22 <span style="color: #949494;">20:06:47</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2022-10-22 <span style="color: #949494;">20:06:47</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2022-10-22 <span style="color: #949494;">20:06:47</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2022-10-22 <span style="color: #949494;">20:06:47</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2022-10-22 <span style="color: #949494;">20:06:47</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table <chr>, method <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S <dbl>, breakpoint_R <dbl>, input <dbl>, interpretation <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># and abbreviated variable names ¹ab_considered, ²mo_input, ³mo_considered,</span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
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<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
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<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: assuming site 'Non-meningitis' for Streptococcus pneumoniae</span>
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<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
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<span class="r-in"><span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
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<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
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<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
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<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: assuming site 'UTI' for Enterobacterales</span>
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<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
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<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
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<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
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<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: assuming site 'UTI' for Enterobacterales</span>
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<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
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<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB ERY</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S R</span>
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<span class="r-in"><span></span></span>
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