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Conduct AMR analysis
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Interpret MIC and Disk Values, or Clean Raw R/SI Data</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/rsi.R" class="external-link"><code>R/rsi.R</code></a></small>
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<div class="d-none name"><code>as.rsi.Rd</code></div>
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<div class="ref-description section level2">
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<p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>S < I < R</code>.</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.rsi</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_rsi_</span></span>
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<span></span>
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<span><span class="fu">is.rsi</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.rsi.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"># S3 method for mic</span></span>
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<span><span class="fu">as.rsi</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<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="st">"EUCAST"</span>,</span>
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<span> uti <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> conserve_capped_values <span class="op">=</span> <span class="cn">FALSE</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="rsi_translation.html">rsi_translation</a></span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for disk</span></span>
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<span><span class="fu">as.rsi</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<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="st">"EUCAST"</span>,</span>
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<span> uti <span class="op">=</span> <span class="cn">FALSE</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="rsi_translation.html">rsi_translation</a></span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for data.frame</span></span>
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<span><span class="fu">as.rsi</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> <span class="va">...</span>,</span>
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<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span>,</span>
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<span> uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> conserve_capped_values <span class="op">=</span> <span class="cn">FALSE</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="rsi_translation.html">rsi_translation</a></span></span>
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<span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>An object of class <code>rsi</code> (inherits from <code>ordered</code>, <code>factor</code>) of length 1.</p>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<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>
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<dt>...</dt>
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<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.rsi()</code> on (supports tidy selection such as <code>column1:column4</code>). Otherwise: arguments passed on to methods.</p></dd>
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<dt>threshold</dt>
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<dd><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, see <em>Examples</em></p></dd>
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<dt>mo</dt>
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<dd><p>any (vector of) text 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>
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<dt>ab</dt>
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<dd><p>any (vector of) text that can be coerced to a valid antimicrobial code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
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<dt>guideline</dt>
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<dd><p>defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the <a href="rsi_translation.html">rsi_translation</a> data set), supports EUCAST (2011-2022) and CLSI (2011-2022), see <em>Details</em></p></dd>
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<dt>uti</dt>
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<dd><p>(Urinary Tract Infection) A vector 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.rsi()</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>conserve_capped_values</dt>
|
|||
|
|
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that MIC values starting with <code>">"</code> (but not <code>">="</code>) must always return "R" , and that MIC values starting with <code>"<"</code> (but not <code>"<="</code>) must always return "S"</p></dd>
|
|||
|
|
|
|||
|
|
|
|||
|
|
<dt>add_intrinsic_resistance</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>reference_data</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="rsi_translation.html">rsi_translation</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="rsi_translation.html">rsi_translation</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>col_mo</dt>
|
|||
|
|
<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to 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>
|
|||
|
|
|
|||
|
|
</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><rsi></code></p>
|
|||
|
|
|
|||
|
|
|
|||
|
|
</div>
|
|||
|
|
<div class="section level2">
|
|||
|
|
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
|||
|
|
|
|||
|
|
<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.rsi()</code> function works in four ways:</p><ol><li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI 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 unclear.</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>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p>
|
|||
|
|
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%>%</span> <span class="fu">mutate_if</span>(is.mic, as.rsi) <span class="co"># until dplyr 1.0.0</span></span>
|
|||
|
|
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%>%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(is.mic), as.rsi)) <span class="co"># since dplyr 1.0.0</span></span></code></pre><p></p></div></li>
|
|||
|
|
<li><p>Operators like "<=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</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>conserve_capped_values = FALSE</code>) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".</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>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p>
|
|||
|
|
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%>%</span> <span class="fu">mutate_if</span>(is.disk, as.rsi) <span class="co"># until dplyr 1.0.0</span></span>
|
|||
|
|
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%>%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(is.disk), as.rsi)) <span class="co"># since dplyr 1.0.0</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.rsi(your_data)</code>.</p></li>
|
|||
|
|
</ol></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 EUCAST (2011-2022) and CLSI (2011-2022).</p>
|
|||
|
|
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2022"</code> or <code>"CLSI 2022"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
|
|||
|
|
</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.rsi()</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>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<div class="section">
|
|||
|
|
<h3 id="machine-readable-interpretation-guidelines">Machine-Readable Interpretation Guidelines<a class="anchor" aria-label="anchor" href="#machine-readable-interpretation-guidelines"></a></h3>
|
|||
|
|
|
|||
|
|
|
|||
|
|
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 20,369 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<div class="section">
|
|||
|
|
<h3 id="other">Other<a class="anchor" aria-label="anchor" href="#other"></a></h3>
|
|||
|
|
|
|||
|
|
|
|||
|
|
<p>The function <code>is.rsi()</code> detects if the input contains class <code><rsi></code>. 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>
|
|||
|
|
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), 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_rsi_</code> is a missing value of the new <code><rsi></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-r-and-s-i">Interpretation of R and S/I<a class="anchor" aria-label="anchor" href="#interpretation-of-r-and-s-i"></a></h2>
|
|||
|
|
|
|||
|
|
|
|||
|
|
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href="https://www.eucast.org/newsiandr/" class="external-link">https://www.eucast.org/newsiandr/</a>).</p><ul><li><p><strong>R = Resistant</strong><br>
|
|||
|
|
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
|
|||
|
|
<li><p><strong>S = Susceptible</strong><br>
|
|||
|
|
A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
|
|||
|
|
<li><p><strong>I = Susceptible, Increased exposure</strong><br>
|
|||
|
|
A microorganism is categorised as <em>Susceptible, Increased exposure</em> when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
|
|||
|
|
</ul><p>This AMR package honours this (new) 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="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
|||
|
|
|
|||
|
|
|
|||
|
|
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</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 × 49</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> date hospit…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </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;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></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>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 B TRUE FALSE FALSE 79 F 858515 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</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="co"># see all R/SI results at a glance</span></span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> date hospital_id ward_icu ward_clinical </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Min. :2002-01-02 A:321 Mode :logical Mode :logical </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> 1st Qu.:2005-07-31 B:663 FALSE:1354 FALSE:536 </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Median :2009-07-31 C:254 TRUE :646 TRUE :1464 </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Mean :2009-11-20 D:762 </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> 3rd Qu.:2014-05-30 </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Max. :2017-12-28 </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> ward_outpatient age gender patient_id </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Mode :logical Min. : 0.00 Length:2000 Length:2000 </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> FALSE:1880 1st Qu.:63.00 Class :character Class :character </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> TRUE :120 Median :74.00 Mode :character Mode :character </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Mean :70.69 </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> 3rd Qu.:82.00 </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Max. :97.00 </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> mo PEN OXA </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class :mo Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <NA> :0 %R :73.7% (n=1201) %R :31.2% (n=114) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Unique:90 %SI :26.3% (n=428) %SI :68.8% (n=251) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> #1 :B_ESCHR_COLI - %S :25.6% (n=417) - %S :68.8% (n=251) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> #2 :B_STPHY_CONS - %I : 0.7% (n=11) - %I : 0.0% (n=0) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> #3 :B_STPHY_AURS </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> FLC AMX AMC </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :29.5% (n=278) %R :59.6% (n=804) %R :23.7% (n=446) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :70.5% (n=665) %SI :40.4% (n=546) %SI :76.3% (n=1433) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :70.5% (n=665) - %S :40.2% (n=543) - %S :71.4% (n=1342) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.2% (n=3) - %I : 4.8% (n=91) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> AMP TZP CZO </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :59.6% (n=804) %R :12.6% (n=126) %R :44.6% (n=199) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :40.4% (n=546) %SI :87.4% (n=875) %SI :55.4% (n=247) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :40.2% (n=543) - %S :86.1% (n=862) - %S :54.9% (n=245) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.2% (n=3) - %I : 1.3% (n=13) - %I : 0.4% (n=2) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> FEP CXM FOX </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :14.2% (n=103) %R :26.3% (n=470) %R :27.4% (n=224) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :85.8% (n=621) %SI :73.7% (n=1319) %SI :72.6% (n=594) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :85.6% (n=620) - %S :72.5% (n=1297) - %S :71.6% (n=586) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.1% (n=1) - %I : 1.2% (n=22) - %I : 1.0% (n=8) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> CTX CAZ CRO </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :15.5% (n=146) %R :66.5% (n=1204) %R :15.5% (n=146) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :84.5% (n=797) %SI :33.5% (n=607) %SI :84.5% (n=797) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :84.4% (n=796) - %S :33.5% (n=607) - %S :84.4% (n=796) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.1% (n=1) - %I : 0.0% (n=0) - %I : 0.1% (n=1) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> GEN TOB AMK </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :24.6% (n=456) %R :34.4% (n=465) %R :63.7% (n=441) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :75.4% (n=1399) %SI :65.6% (n=886) %SI :36.3% (n=251) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :74.0% (n=1372) - %S :65.1% (n=879) - %S :36.3% (n=251) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 1.5% (n=27) - %I : 0.5% (n=7) - %I : 0.0% (n=0) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> KAN TMP SXT </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :100.0% (n=471) %R :38.1% (n=571) %R :20.5% (n=361) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI : 0.0% (n=0) %SI :61.9% (n=928) %SI :79.5% (n=1398) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S : 0.0% (n=0) - %S :61.2% (n=918) - %S :79.1% (n=1392) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.7% (n=10) - %I : 0.3% (n=6) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> NIT FOS LNZ </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :17.1% (n=127) %R :42.2% (n=148) %R :69.3% (n=709) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :82.9% (n=616) %SI :57.8% (n=203) %SI :30.7% (n=314) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :76.0% (n=565) - %S :57.8% (n=203) - %S :30.7% (n=314) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 6.9% (n=51) - %I : 0.0% (n=0) - %I : 0.0% (n=0) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> CIP MFX VAN </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :16.2% (n=228) %R :33.6% (n=71) %R :38.3% (n=712) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :83.8% (n=1181) %SI :66.4% (n=140) %SI :61.7% (n=1149) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :78.9% (n=1112) - %S :64.5% (n=136) - %S :61.7% (n=1149) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 4.9% (n=69) - %I : 1.9% (n=4) - %I : 0.0% (n=0) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> TEC TCY TGC </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :75.7% (n=739) %R :29.8% (n=357) %R :12.7% (n=101) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :24.3% (n=237) %SI :70.3% (n=843) %SI :87.3% (n=697) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :24.3% (n=237) - %S :68.3% (n=820) - %S :87.3% (n=697) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 1.9% (n=23) - %I : 0.0% (n=0) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> DOX ERY CLI </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :27.7% (n=315) %R :57.2% (n=1084) %R :61.2% (n=930) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :72.3% (n=821) %SI :42.8% (n=810) %SI :38.8% (n=590) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :71.7% (n=814) - %S :42.3% (n=801) - %S :38.6% (n=586) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.6% (n=7) - %I : 0.5% (n=9) - %I : 0.3% (n=4) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> AZM IPM MEM </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :57.2% (n=1084) %R : 6.2% (n=55) %R : 5.9% (n=49) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :42.8% (n=810) %SI :93.8% (n=834) %SI :94.1% (n=780) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :42.3% (n=801) - %S :92.7% (n=824) - %S :94.1% (n=780) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.5% (n=9) - %I : 1.1% (n=10) - %I : 0.0% (n=0) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> MTR CHL COL </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R :14.7% (n=5) %R :21.4% (n=33) %R :81.2% (n=1331) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :85.3% (n=29) %SI :78.6% (n=121) %SI :18.8% (n=309) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :85.3% (n=29) - %S :78.6% (n=121) - %S :18.8% (n=309) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.0% (n=0) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> MUP RIF </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %R : 5.9% (n=16) %R :69.6% (n=698) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> %SI :94.1% (n=254) %SI :30.4% (n=305) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %S :93.0% (n=251) - %S :30.2% (n=303) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> - %I : 1.1% (n=3) - %I : 0.2% (n=2) </span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></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"># a whole data set, even with combined MIC values and disk zones</span></span></span>
|
|||
|
|
<span class="r-in"><span><span class="va">df</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>microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
|
|||
|
|
<span class="r-in"><span> AMP <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> CIP <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> GEN <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> TOB <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> NIT <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">32</span><span class="op">)</span>,</span></span>
|
|||
|
|
<span class="r-in"><span> ERY <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span></span></span>
|
|||
|
|
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'microorganism' as input for `col_mo`.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'AMP' (AMP, ampicillin) according to</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'CIP' (CIP, ciprofloxacin) according</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'GEN' (GEN, gentamicin)</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'TOB' (TOB, tobramycin)</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (NIT, nitrofurantoin) according</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Assigning class <rsi> to already clean column 'ERY' (erythromycin)...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB NIT ERY</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S <NA> R</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.rsi</span><span class="op">(</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 class="op">)</span></span></span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "S. pneumoniae" (assuming</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> Streptococcus pneumoniae). Run `mo_uncertainties()` to review this.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) according to EUCAST</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></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.rsi</span><span class="op">(</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 class="op">)</span></span></span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'ampicillin' according to EUCAST</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></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="co"># \donttest{</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">df</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.rsi</span><span class="op">)</span></span></span>
|
|||
|
|
<span class="r-in"><span> <span class="va">df</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.rsi</span><span class="op">)</span></span></span>
|
|||
|
|
<span class="r-in"><span> <span class="va">df</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">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span></span></span>
|
|||
|
|
<span class="r-in"><span> <span class="va">df</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">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></span></span>
|
|||
|
|
<span class="r-in"><span> <span class="va">df</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">AMP</span><span class="op">:</span><span class="va">TOB</span>, <span class="va">as.rsi</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="va">df</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">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="va">.</span><span class="op">$</span><span class="va">microorganism</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>mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
|||
|
|
<span class="r-in"><span> NIT <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 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.rsi</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>mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
|||
|
|
<span class="r-in"><span> NIT <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 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.rsi</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</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">AMP</span><span class="op">:</span><span class="va">NIT</span><span class="op">)</span>, <span class="va">as.rsi</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-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) based on</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) based on</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) based on</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) based on</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) based on</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) based on</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) according to EUCAST</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) according to</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) according</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) according</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (NIT, nitrofurantoin) according</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> infection.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> Use `as.rsi(uti = FALSE)` to prevent this.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (NIT, nitrofurantoin) according</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) according to EUCAST</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) according to</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) according</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) according</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) according to</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
|||
|
|
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB NIT ERY</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S S R</span>
|
|||
|
|
<span class="r-in"><span></span></span>
|
|||
|
|
<span class="r-in"><span><span class="co"># For CLEANING existing R/SI values ------------------------------------</span></span></span>
|
|||
|
|
<span class="r-in"><span></span></span>
|
|||
|
|
<span class="r-in"><span><span class="fu">as.rsi</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">"I"</span>, <span class="st">"R"</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 `as.rsi()`: 3 results truncated (50%) that were invalid antimicrobial</span>
|
|||
|
|
<span class="r-wrn co"><span class="r-pr">#></span> interpretations: "A", "B" and "C"</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] S I R <NA> <NA> <NA></span>
|
|||
|
|
<span class="r-in"><span><span class="fu">as.rsi</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 <rsi></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] S</span>
|
|||
|
|
<span class="r-in"><span><span class="va">rsi_data</span> <span class="op"><-</span> <span class="fu">as.rsi</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.rsi</span><span class="op">(</span><span class="va">rsi_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">rsi_data</span><span class="op">)</span> <span class="co"># for percentages</span></span></span>
|
|||
|
|
<span class="r-plt img"><img src="as.rsi-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">rsi_data</span><span class="op">)</span> <span class="co"># for frequencies</span></span></span>
|
|||
|
|
<span class="r-plt img"><img src="as.rsi-2.png" alt="" width="700" height="433"></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.rsi</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.rsi</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 `rsi`:</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.rsi.eligible</span>, <span class="va">as.rsi</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: </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.rsi.eligible), as.rsi))</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 × 49</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> date hospit…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </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;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></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>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 B TRUE FALSE FALSE 79 F 858515 B_STPHY_EPDR</span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
|||
|
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</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"><h2>On this page</h2>
|
|||
|
|
</nav></aside></div>
|
|||
|
|
|
|||
|
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|
|||
|
|
<footer><div class="pkgdown-footer-left">
|
|||
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.png" style="max-width: 200px;"></a></p>
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