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<img src="../logo.svg" class="logo" alt=""><h1>Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/sir.R" class="external-link"><code>R/sir.R</code></a></small>
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<div class="d-none name"><code>as.sir.Rd</code></div>
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<div class="ref-description section level2">
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<p>Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. <code>as.sir()</code> transforms the input to a new class <code>sir</code>, which is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> containing the levels <code>S</code>, <code>SDD</code>, <code>I</code>, <code>R</code>, <code>NI</code>.</p>
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<p>Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see <em>Details</em>. All breakpoints used for interpretation are available in our <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="va">NA_sir_</span></span>
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<span></span>
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<span><span class="fu">is.sir</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">is_sir_eligible</span><span class="op">(</span><span class="va">x</span>, threshold <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># Default S3 method</span></span>
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<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, S <span class="op">=</span> <span class="st">"^(S|U)+$"</span>, I <span class="op">=</span> <span class="st">"^(I)+$"</span>, R <span class="op">=</span> <span class="st">"^(R)+$"</span>,</span>
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<span> NI <span class="op">=</span> <span class="st">"^(N|NI|V)+$"</span>, SDD <span class="op">=</span> <span class="st">"^(SDD|D|H)+$"</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>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for class 'mic'</span></span>
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<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</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> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>, uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> capped_mic_handling <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_capped_mic_handling"</span>, <span class="st">"standard"</span><span class="op">)</span>,</span>
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<span> add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
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<span> substitute_missing_r_breakpoint <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_substitute_missing_r_breakpoint"</span>,</span>
|
||
<span> <span class="cn">FALSE</span><span class="op">)</span>, include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
|
||
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
|
||
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</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>,</span>
|
||
<span> conserve_capped_values <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="co"># S3 method for class 'disk'</span></span>
|
||
<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
|
||
<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>, uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||
<span> add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
|
||
<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
|
||
<span> substitute_missing_r_breakpoint <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_substitute_missing_r_breakpoint"</span>,</span>
|
||
<span> <span class="cn">FALSE</span><span class="op">)</span>, include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
|
||
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
|
||
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</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>,</span>
|
||
<span> <span class="va">...</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="co"># S3 method for class 'data.frame'</span></span>
|
||
<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||
<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>, uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||
<span> capped_mic_handling <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_capped_mic_handling"</span>, <span class="st">"standard"</span><span class="op">)</span>,</span>
|
||
<span> add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
|
||
<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
|
||
<span> substitute_missing_r_breakpoint <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_substitute_missing_r_breakpoint"</span>,</span>
|
||
<span> <span class="cn">FALSE</span><span class="op">)</span>, include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
|
||
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
|
||
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</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>,</span>
|
||
<span> parallel <span class="op">=</span> <span class="cn">FALSE</span>, max_cores <span class="op">=</span> <span class="op">-</span><span class="fl">1</span>, conserve_capped_values <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
|
||
</div>
|
||
|
||
<div class="section level2">
|
||
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
|
||
<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2025, <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>
|
||
<li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2025, <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>
|
||
<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2025, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01/" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01/</a>.</p></li>
|
||
<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2025, <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>
|
||
<li><p><strong>WHONET</strong> as a source for machine-reading the clinical breakpoints (<a href="https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet">read more here</a>), 1989-2025, <em>WHO Collaborating Centre for Surveillance of Antimicrobial Resistance</em>. <a href="https://whonet.org/" class="external-link">https://whonet.org/</a>.</p></li>
|
||
</ul></div>
|
||
<div class="section level2">
|
||
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
|
||
|
||
|
||
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
|
||
<dd><p>Vector of values (for class <code><a href="as.mic.html">mic</a></code>: MIC values in mg/L, for class <code><a href="as.disk.html">disk</a></code>: a disk diffusion radius in millimetres).</p></dd>
|
||
|
||
|
||
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
|
||
<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: names of columns to apply <code>as.sir()</code> on (supports tidy selection such as <code>column1:column4</code>). Otherwise: arguments passed on to methods.</p></dd>
|
||
|
||
|
||
<dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a></dt>
|
||
<dd><p>Maximum fraction of invalid antimicrobial interpretations of <code>x</code>, see <em>Examples</em>.</p></dd>
|
||
|
||
|
||
<dt id="arg-s-i-r-ni-sdd">S, I, R, NI, SDD<a class="anchor" aria-label="anchor" href="#arg-s-i-r-ni-sdd"></a></dt>
|
||
<dd><p>A case-independent <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to translate input to this result. This regular expression will be run <em>after</em> all non-letters and whitespaces are removed from the input.</p></dd>
|
||
|
||
|
||
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
|
||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to print information about the process, defaults to <code>TRUE</code> only in <a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive sessions</a>.</p></dd>
|
||
|
||
|
||
<dt id="arg-mo">mo<a class="anchor" aria-label="anchor" href="#arg-mo"></a></dt>
|
||
<dd><p>A vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s that can be coerced to valid microorganism codes with <code><a href="as.mo.html">as.mo()</a></code>, can be left empty to determine it automatically.</p></dd>
|
||
|
||
|
||
<dt id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></dt>
|
||
<dd><p>A vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>
|
||
|
||
|
||
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
|
||
<dd><p>A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2025 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the package option <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2025) and CLSI (2011-2025), see <em>Details</em>. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.</p></dd>
|
||
|
||
|
||
<dt id="arg-uti">uti<a class="anchor" aria-label="anchor" href="#arg-uti"></a></dt>
|
||
<dd><p>(Urinary Tract Infection) a vector (or column name) with <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.sir()</code> on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, this can also be a column containing <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See <em>Examples</em>.</p></dd>
|
||
|
||
|
||
<dt id="arg-capped-mic-handling">capped_mic_handling<a class="anchor" aria-label="anchor" href="#arg-capped-mic-handling"></a></dt>
|
||
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> string that controls how MIC values with a cap (i.e., starting with <code><</code>, <code><=</code>, <code>></code>, or <code>>=</code>) are interpreted. Supports the following options:</p>
|
||
<p><code>"none"</code></p><ul><li><p><code><=</code> and <code>>=</code> are treated as-is.</p></li>
|
||
<li><p><code><</code> and <code>></code> are treated as-is.</p></li>
|
||
</ul><p><code>"conservative"</code></p><ul><li><p><code><=</code> and <code>>=</code> return <code>"NI"</code> (non-interpretable) if the MIC is within the breakpoint guideline range.</p></li>
|
||
<li><p><code><</code> always returns <code>"S"</code>, and <code>></code> always returns <code>"R"</code>.</p></li>
|
||
</ul><p><code>"standard"</code> (default)</p><ul><li><p><code><=</code> and <code>>=</code> return <code>"NI"</code> (non-interpretable) if the MIC is within the breakpoint guideline range.</p></li>
|
||
<li><p><code><</code> and <code>></code> are treated as-is.</p></li>
|
||
</ul><p><code>"inverse"</code></p><ul><li><p><code><=</code> and <code>>=</code> are treated as-is.</p></li>
|
||
<li><p><code><</code> always returns <code>"S"</code>, and <code>></code> always returns <code>"R"</code>.</p></li>
|
||
</ul><p>The default <code>"standard"</code> setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option <code><a href="AMR-options.html">AMR_capped_mic_handling</a></code>.</p></dd>
|
||
|
||
|
||
<dt id="arg-add-intrinsic-resistance">add_intrinsic_resistance<a class="anchor" aria-label="anchor" href="#arg-add-intrinsic-resistance"></a></dt>
|
||
<dd><p><em>(only useful when using a EUCAST guideline)</em> a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, that itself is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021).</p></dd>
|
||
|
||
|
||
<dt id="arg-reference-data">reference_data<a class="anchor" aria-label="anchor" href="#arg-reference-data"></a></dt>
|
||
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for interpretation, which defaults to the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set (same column names and column types). Please note that the <code>guideline</code> argument will be ignored when <code>reference_data</code> is manually set.</p></dd>
|
||
|
||
|
||
<dt id="arg-substitute-missing-r-breakpoint">substitute_missing_r_breakpoint<a class="anchor" aria-label="anchor" href="#arg-substitute-missing-r-breakpoint"></a></dt>
|
||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is <code>FALSE</code>. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning that the outcome can only be <code>"S"</code> or <code>NA</code>. Setting this to <code>TRUE</code> will convert the <code>NA</code>s in these cases to <code>"R"</code>. Can also be set with the package option <code><a href="AMR-options.html">AMR_substitute_missing_r_breakpoint</a></code>.</p></dd>
|
||
|
||
|
||
<dt id="arg-include-screening">include_screening<a class="anchor" aria-label="anchor" href="#arg-include-screening"></a></dt>
|
||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that clinical breakpoints for screening are allowed - the default is <code>FALSE</code>. Can also be set with the package option <code><a href="AMR-options.html">AMR_include_screening</a></code>.</p></dd>
|
||
|
||
|
||
<dt id="arg-include-pkpd">include_PKPD<a class="anchor" aria-label="anchor" href="#arg-include-pkpd"></a></dt>
|
||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>. Can also be set with the package option <code><a href="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd>
|
||
|
||
|
||
<dt id="arg-breakpoint-type">breakpoint_type<a class="anchor" aria-label="anchor" href="#arg-breakpoint-type"></a></dt>
|
||
<dd><p>The type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the package option <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd>
|
||
|
||
|
||
<dt id="arg-host">host<a class="anchor" aria-label="anchor" href="#arg-host"></a></dt>
|
||
<dd><p>A vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s to indicate the host. Only useful for veterinary breakpoints, as it requires <code>breakpoint_type = "animal"</code>. The values can be any text resembling the animal species, even in any of the 28 supported languages of this package. For foreign languages, be sure to set the language with <code><a href="translate.html">set_AMR_locale()</a></code> (though it will be automatically guessed based on the system language).</p></dd>
|
||
|
||
|
||
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
|
||
<dd><p>Language to convert values set in <code>host</code> when using animal breakpoints. Use one of these supported language names or <a href="https://en.wikipedia.org/wiki/ISO_639-1" class="external-link">ISO 639-1 codes</a>: English (en), Arabic (ar), Bengali (bn), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Hindi (hi), Indonesian (id), Italian (it), Japanese (ja), Korean (ko), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swahili (sw), Swedish (sv), Turkish (tr), Ukrainian (uk), Urdu (ur), or Vietnamese (vi).</p></dd>
|
||
|
||
|
||
<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
|
||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that all notes should be printed during interpretation of MIC values or disk diffusion values.</p></dd>
|
||
|
||
|
||
<dt id="arg-conserve-capped-values">conserve_capped_values<a class="anchor" aria-label="anchor" href="#arg-conserve-capped-values"></a></dt>
|
||
<dd><p>Deprecated, use <code>capped_mic_handling</code> instead.</p></dd>
|
||
|
||
|
||
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
|
||
<dd><p>Column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
|
||
|
||
|
||
<dt id="arg-parallel">parallel<a class="anchor" aria-label="anchor" href="#arg-parallel"></a></dt>
|
||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. This requires no additional packages, as the used <code>parallel</code> package is part of base <span style="R">R</span>. On Windows and on <span style="R">R</span> < 4.0.0 <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> will be used, in all other cases the more efficient <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> will be used.</p></dd>
|
||
|
||
|
||
<dt id="arg-max-cores">max_cores<a class="anchor" aria-label="anchor" href="#arg-max-cores"></a></dt>
|
||
<dd><p>Maximum number of cores to use if <code>parallel = TRUE</code>. Use a negative value to subtract that number from the available number of cores, e.g. a value of <code>-2</code> on an 8-core machine means that at most 6 cores will be used. Defaults to <code>-1</code>. There will never be used more cores than variables to analyse. The available number of cores are detected using <code><a href="https://parallelly.futureverse.org/reference/availableCores.html" class="external-link">parallelly::availableCores()</a></code> if that package is installed, and base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">parallel::detectCores()</a></code> otherwise.</p></dd>
|
||
|
||
|
||
<dt id="arg-clean">clean<a class="anchor" aria-label="anchor" href="#arg-clean"></a></dt>
|
||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether previously stored results should be forgotten after returning the 'logbook' with results.</p></dd>
|
||
|
||
</dl></div>
|
||
<div class="section level2">
|
||
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
|
||
<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with new class <code>sir</code></p>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||
<p><em>Note: The clinical breakpoints in this package were validated through, and imported from, <a href="https://whonet.org" class="external-link">WHONET</a>. The public use of this <code>AMR</code> package has been endorsed by both CLSI and EUCAST. See <a href="clinical_breakpoints.html">clinical_breakpoints</a> for more information.</em></p><div class="section">
|
||
<h3 id="how-it-works">How it Works<a class="anchor" aria-label="anchor" href="#how-it-works"></a></h3>
|
||
|
||
|
||
<p>The <code>as.sir()</code> function can work in four ways:</p><ol><li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain valid values, namely: <strong>S</strong> for susceptible, <strong>I</strong> for intermediate or 'susceptible, increased exposure', <strong>R</strong> for resistant, <strong>NI</strong> for non-interpretable, and <strong>SDD</strong> for susceptible dose-dependent. Each of these can be set using a <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a>. Furthermore, <code>as.sir()</code> will try its best to clean with some intelligence. For example, mixed values with SIR interpretations and MIC values such as <code>"<0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is invalid.</p></li>
|
||
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href="as.mic.html">as.mic()</a></code>, that also gives your columns the new data class <code><a href="as.mic.html">mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Example to apply using <code>dplyr</code>:</p>
|
||
<p></p><div class="sourceCode r"><pre><code><span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span><span class="op">)</span></span>
|
||
<span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span>
|
||
<span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>, ab <span class="op">=</span> <span class="st">"column_with_antibiotics"</span>, mo <span class="op">=</span> <span class="st">"column_with_microorganisms"</span><span class="op">)</span></span>
|
||
<span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>, ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cipro"</span>, <span class="st">"ampicillin"</span>, <span class="va">...</span><span class="op">)</span>, mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="st">"K. pneumoniae"</span>, <span class="va">...</span><span class="op">)</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="co"># for veterinary breakpoints, also set `host`:</span></span>
|
||
<span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>, host <span class="op">=</span> <span class="st">"column_with_animal_species"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="co"># fast processing with parallel computing:</span></span>
|
||
<span><span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="va">your_data</span>, <span class="va">...</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre><p></p></div></li>
|
||
<li><p>Operators like "<=" will be stripped before interpretation. When using <code>capped_mic_handling = "conservative"</code>, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>capped_mic_handling = "standard"</code>) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".</p></li>
|
||
<li><p><strong>Note:</strong> When using CLSI as the guideline, MIC values must be log2-based doubling dilutions. Values not in this format, will be automatically rounded up to the nearest log2 level as CLSI instructs, and a warning will be thrown.</p></li>
|
||
</ul></li>
|
||
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href="as.disk.html">as.disk()</a></code>, that also gives your columns the new data class <code><a href="as.disk.html">disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Example to apply using <code>dplyr</code>:</p>
|
||
<p></p><div class="sourceCode r"><pre><code><span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.disk</span>, <span class="va">as.sir</span><span class="op">)</span></span>
|
||
<span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.disk</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span>
|
||
<span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.disk</span>, <span class="va">as.sir</span>, ab <span class="op">=</span> <span class="st">"column_with_antibiotics"</span>, mo <span class="op">=</span> <span class="st">"column_with_microorganisms"</span><span class="op">)</span></span>
|
||
<span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.disk</span>, <span class="va">as.sir</span>, ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cipro"</span>, <span class="st">"ampicillin"</span>, <span class="va">...</span><span class="op">)</span>, mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="st">"K. pneumoniae"</span>, <span class="va">...</span><span class="op">)</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="co"># for veterinary breakpoints, also set `host`:</span></span>
|
||
<span><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.disk</span>, <span class="va">as.sir</span>, host <span class="op">=</span> <span class="st">"column_with_animal_species"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="co"># fast processing with parallel computing:</span></span>
|
||
<span><span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="va">your_data</span>, <span class="va">...</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre><p></p></div></li>
|
||
</ul></li>
|
||
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.sir(your_data)</code>.</p></li>
|
||
</ol><p><strong>For points 2, 3 and 4: Use <code>sir_interpretation_history()</code></strong> to retrieve a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with all results of all previous <code>as.sir()</code> calls. It also contains notes about interpretation, and the exact input and output values.</p>
|
||
</div>
|
||
|
||
<div class="section">
|
||
<h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
|
||
|
||
|
||
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2025 and CLSI 2011-2025;</p></li>
|
||
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2025 and CLSI 2019-2025;</p></li>
|
||
<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.</p></li>
|
||
</ul><p>The <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2025"</code> or <code>"CLSI 2025"</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. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.</p>
|
||
<p>You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
|
||
<p>It is also possible to set the default guideline with the package option <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p>
|
||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span>
|
||
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI 2018"</span>)</span>
|
||
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"EUCAST 2020"</span>)</span>
|
||
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a> <span class="co"># or to reset:</span></span>
|
||
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="cn">NULL</span>)</span></code></pre><p></p></div>
|
||
</div>
|
||
|
||
<div class="section">
|
||
<h3 id="working-with-veterinary-breakpoints">Working with Veterinary Breakpoints<a class="anchor" aria-label="anchor" href="#working-with-veterinary-breakpoints"></a></h3>
|
||
|
||
|
||
<p>When using veterinary breakpoints (i.e., setting <code>breakpoint_type = "animal"</code>), a column with animal species must be available or set manually using the <code>host</code> argument. The column must contain names like "dogs", "cats", "cattle", "swine", "horses", "poultry", or "aquatic". Other animal names like "goats", "rabbits", or "monkeys" are also recognised but may not be available in all guidelines. Matching is case-insensitive and accepts Latin-based synonyms (e.g., "bovine" for cattle and "canine" for dogs).</p>
|
||
<p>Regarding choice of veterinary guidelines, these might be the best options to set before analysis:</p>
|
||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span>
|
||
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_breakpoint_type =</span> <span class="st">"animal"</span>)</span></code></pre><p></p></div>
|
||
</div>
|
||
|
||
<div class="section">
|
||
<h3 id="after-interpretation">After Interpretation<a class="anchor" aria-label="anchor" href="#after-interpretation"></a></h3>
|
||
|
||
|
||
<p>After using <code>as.sir()</code>, you can use the <code><a href="eucast_rules.html">eucast_rules()</a></code> defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
|
||
<p>To determine which isolates are multi-drug resistant, be sure to run <code><a href="mdro.html">mdro()</a></code> (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about <a href="mdro.html">interpreting multidrug-resistant organisms here</a>.</p>
|
||
</div>
|
||
|
||
<div class="section">
|
||
<h3 id="other">Other<a class="anchor" aria-label="anchor" href="#other"></a></h3>
|
||
|
||
|
||
<p>The function <code>is.sir()</code> detects if the input contains class <code>sir</code>. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> or <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>, it iterates over all columns/items and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
|
||
<p>The base R function <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> can be used to retrieve quantitative values from a <code>sir</code> object: <code>"S"</code> = 1, <code>"I"</code>/<code>"SDD"</code> = 2, <code>"R"</code> = 3. All other values are rendered <code>NA</code> . <strong>Note:</strong> Do not use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code>, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.</p>
|
||
<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a column contains at most 5% potentially invalid antimicrobial interpretations, and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
|
||
</div>
|
||
|
||
<p><code>NA_sir_</code> is a missing value of the new <code>sir</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
|
||
|
||
|
||
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>).</p>
|
||
<p>This AMR package follows insight; use <code><a href="proportion.html">susceptibility()</a></code> (equal to <code><a href="proportion.html">proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href="count.html">count_susceptible()</a></code> (equal to <code><a href="count.html">count_SI()</a></code>) to count susceptible isolates.</p>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="download-our-reference-data">Download Our Reference Data<a class="anchor" aria-label="anchor" href="#download-our-reference-data"></a></h2>
|
||
|
||
|
||
<p>All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.</p>
|
||
<p>For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.</p>
|
||
<p>Visit <a href="https://amr-for-r.org/articles/datasets.html">our website for direct download links</a>, or explore the actual files in <a href="https://github.com/msberends/AMR/tree/main/data-raw/datasets" class="external-link">our GitHub repository</a>.</p>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||
<div class="dont-index"><p><code><a href="as.mic.html">as.mic()</a></code>, <code><a href="as.disk.html">as.disk()</a></code>, <code><a href="as.mo.html">as.mo()</a></code></p></div>
|
||
</div>
|
||
|
||
<div class="section level2">
|
||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">example_isolates</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 1,990 more rows</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span><span class="op">)</span> <span class="co"># see all SIR results at a glance</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Min. :2002-01-02 Length:2000 Min. : 0.00 Length:2000 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 1st Qu.:2005-07-31 Class :character 1st Qu.:63.00 Class :character </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Median :2009-07-31 Mode :character Median :74.00 Mode :character </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Mean :2009-11-20 Mean :70.69 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 3rd Qu.:2014-05-30 3rd Qu.:82.00 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Max. :2017-12-28 Max. :97.00 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> ward mo PEN </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Length:2000 Class :mo Class:sir </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class :character <NA> :0 %S :25.6% (n=417) </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Mode :character Unique:90 %SDD : 0.0% (n=0) </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> #1 :B_ESCHR_COLI %I : 0.7% (n=11) </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> #2 :B_STPHY_CONS %R :73.7% (n=1201) </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> #3 :B_STPHY_AURS %NI : 0.0% (n=0) </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> %S :68.8% (n=251) %S :70.5% (n=665) %S :40.2% (n=543) </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.2% (n=3) </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> %R :31.2% (n=114) %R :29.5% (n=278) %R :59.6% (n=804) </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># create some example data sets, with combined MIC values and disk zones</span></span></span>
|
||
<span class="r-in"><span><span class="va">df_wide</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
|
||
<span class="r-in"><span> amoxicillin <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">8</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> cipro <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.256</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> tobra <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">16</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> genta <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> ERY <span class="op">=</span> <span class="st">"R"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="va">df_long</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> bacteria <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> antibiotic <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"amoxicillin"</span>, <span class="st">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> mics <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.01</span>, <span class="fl">1</span>, <span class="fl">4</span>, <span class="fl">8</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> disks <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">6</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"EUCAST 2021"</span>, <span class="st">"EUCAST 2022"</span>, <span class="st">"EUCAST 2023"</span>, <span class="st">"EUCAST 2024"</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="co"># and clean previous SIR interpretation logs</span></span></span>
|
||
<span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># most basic application:</span></span></span>
|
||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta ERY</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S R</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
|
||
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||
<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;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2025-05-12 <span style="color: #949494;">10:40:00</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2025-05-12 <span style="color: #949494;">10:40:00</span> 1 MIC cipro Escherich… human 0.256 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2025-05-12 <span style="color: #949494;">10:40:00</span> 1 DISK tobra Escherich… human 16 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2025-05-12 <span style="color: #949494;">10:40:01</span> 1 DISK genta Escherich… human 18 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||
<span class="r-in"><span><span class="co"># using parallel computing, which is available in base R:</span></span></span>
|
||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Returning previously coerced values for various antimicrobials. Run</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> </span><span style="color: #0000BB; background-color: #EEEEEE;">ab_reset_session()</span><span style="color: #0000BB;"> to reset this. This note will be shown once per</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> session.</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Running in parallel mode using 3 out of 4 cores, on columns '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">',</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">', '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">', '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">', and '</span><span style="color: #0000BB; font-weight: bold;">ERY</span><span style="color: #0000BB;">'...</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> DONE</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> to retrieve a logbook with all details</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> of the breakpoint interpretations.</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta ERY</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S R</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co">## Using dplyr -------------------------------------------------</span></span></span>
|
||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># approaches that all work without additional arguments:</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">|</span> <span class="fu"><a href="as.disk.html">is.disk</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">amoxicillin</span><span class="op">:</span><span class="va">tobra</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">amoxicillin</span><span class="op">:</span><span class="va">tobra</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># approaches that all work with additional arguments:</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="co"># given a certain data type, e.g. MIC values</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
|
||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"guideline"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
|
||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"CLSI"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">}</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="co"># given certain columns, e.g. from 'cipro' to 'genta'</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">cipro</span><span class="op">:</span><span class="va">genta</span><span class="op">)</span>, <span class="va">as.sir</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"CLSI"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> <span class="va">cipro</span><span class="op">:</span><span class="va">genta</span>,</span></span>
|
||
<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"CLSI"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">}</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># for veterinary breakpoints, add 'host':</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_long</span><span class="op">$</span><span class="va">animal_species</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cats"</span>, <span class="st">"dogs"</span>, <span class="st">"horses"</span>, <span class="st">"cattle"</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="co"># given a certain data type, e.g. MIC values</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
|
||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
|
||
<span class="r-in"><span> host <span class="op">=</span> <span class="st">"animal_species"</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"CLSI"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
|
||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
|
||
<span class="r-in"><span> host <span class="op">=</span> <span class="st">"animal_species"</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"CLSI"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">}</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">cipro</span><span class="op">:</span><span class="va">genta</span><span class="op">)</span>, <span class="va">as.sir</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
|
||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
|
||
<span class="r-in"><span> host <span class="op">=</span> <span class="st">"animal_species"</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"CLSI"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> <span class="va">cipro</span><span class="op">:</span><span class="va">genta</span>,</span></span>
|
||
<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"bacteria"</span>,</span></span>
|
||
<span class="r-in"><span> host <span class="op">=</span> <span class="st">"animal_species"</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"CLSI"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">}</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># to include information about urinary tract infections (UTI)</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||
<span class="r-in"><span> nitrofuratoin <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> from_the_bladder <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu">as.sir</span><span class="op">(</span>uti <span class="op">=</span> <span class="st">"from_the_bladder"</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||
<span class="r-in"><span> nitrofuratoin <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> specimen <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"urine"</span>, <span class="st">"blood"</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu">as.sir</span><span class="op">(</span><span class="op">)</span> <span class="co"># automatically determines urine isolates</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">cipro</span><span class="op">:</span><span class="va">genta</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `mics = (function (x, ...) ...`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin),</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin),</span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta ERY</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli 8 <NA> S S R</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co">## Using base R ------------------------------------------------</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># for single values</span></span></span>
|
||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S. pneumoniae"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMP"</span>,</span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"Strep pneu"</span>, <span class="co"># `mo` will be coerced with as.mo()</span></span></span>
|
||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
|
||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values -------------------------------------</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 3 results in index '20' truncated (38%) that were invalid</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> antimicrobial interpretations: "A", "B", and "C"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] S SDD I R NI <NA> <NA> <NA></span>
|
||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"<= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] S</span>
|
||
<span class="r-in"><span><span class="va">sir_data</span> <span class="op"><-</span> <span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="fl">474</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"I"</span>, <span class="fl">36</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"R"</span>, <span class="fl">370</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="fu">is.sir</span><span class="op">(</span><span class="va">sir_data</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
|
||
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">sir_data</span><span class="op">)</span> <span class="co"># for percentages</span></span></span>
|
||
<span class="r-plt img"><img src="as.sir-1.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot</a></span><span class="op">(</span><span class="va">sir_data</span><span class="op">)</span> <span class="co"># for frequencies</span></span></span>
|
||
<span class="r-plt img"><img src="as.sir-2.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># as common in R, you can use as.integer() to return factor indices:</span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 3 4 5 NA</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># but for computational use, as.double() will return 1 for S, 2 for I/SDD, and 3 for R:</span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double</a></span><span class="op">(</span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 2 3 NA NA</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># the dplyr way</span></span></span>
|
||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">PEN</span><span class="op">:</span><span class="va">RIF</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># same:</span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">PEN</span><span class="op">:</span><span class="va">RIF</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># fastest way to transform all columns with already valid AMR results to class `sir`:</span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is_sir_eligible</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># since dplyr 1.0.0, this can also be the more impractical:</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># example_isolates %>%</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># mutate(across(where(is_sir_eligible), as.sir))</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 1,990 more rows</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</span></span>
|
||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||
</code></pre></div>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||
</nav></aside></div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
|
||
</div>
|
||
|
||
</footer></div>
|
||
|
||
|
||
|
||
|
||
|
||
</body></html>
|
||
|